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Downgrade networkx dependency #6094

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merged 1 commit into from Sep 26, 2017

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vladsaveliev commented Sep 21, 2017

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

Networkx has recently been updated to 2.0, which is incompatible with colormath spectra dependency (see ewels/MultiQC#561 and
ewels/MultiQC#592). Until a new colormath version is released, we have to downgrade networkx dependency for MultiQC.

cc @ewels

Downgrade networkx dependency
Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.
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vladsaveliev commented Sep 22, 2017

@ewels, travis still fails because of that Click error here #5541 and here #5888, but as far as I understand it's just Travis related issue and the recipe looks good. Do you have any suggestions how we proceed and get this and #5888 merged?

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ewels commented Sep 22, 2017

Umm, hope that someone from @bioconda/core can help and come up with a long term solution where the locale is set in the busybox..? ;)

But otherwise I guess our only option is to go back to skipping the python 3 build:

build:
  skip: true  # [py3k]
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ewels commented Sep 22, 2017

ps.. Other option could possibly be to just remove all tests? Then at least it should build for people using conda versions on their systems, even if the docker containers are broken. Thoughts @bioconda/core ?

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bgruening commented Sep 23, 2017

@ewels I will have finished the R3.4 migration soon and will have a look at it.
Sorry that it takes so long.

@daler daler referenced this pull request Sep 26, 2017

Merged

locale-gen en_US.UTF-8 #3

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daler commented Sep 26, 2017

@bgruening @vladsaveliev @ewels I think the issue is that we have 3 docker containers in play which have mutually incompatible locale settings.

conda build is run on condaforge/linux-anvil. This has en_US.UTF-8 but does not have C.UTF-8:

docker run -it condaforge/linux-anvil
(root) [root@25975080fb60 /]# export LC_ALL=C.UTF-8
bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8): No such file or directory
bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)

(root) [root@123012ab5f3d /]# export LC_ALL="en_US.UTF-8"  # works fine

mulled-build by default uses busybox, which has no locale installed.

The extended-base container has C.UTF-8 but not en_US.UTF-8:

docker run -it bitnami/minideb:jessie
root@cf34d7a492d4:/# LC_ALL=C.UTF-8 # works fine
root@cf34d7a492d4:/# export LC_ALL=en_US.UTF-8 
bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory

I think this should fix it: bioconda/bioconda-extended-base-image#3

xrefs #5842, #5541, #5369, #5249, #4811

@daler daler merged commit 371548f into bioconda:master Sep 26, 2017

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daler commented Sep 26, 2017

Whoo!

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vladsaveliev commented Sep 26, 2017

That's awesome. Thanks for sorting it out!

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ewels commented Sep 26, 2017

Fantastic! Python3 conda builds again! 🎉 Awesome stuff @daler, thanks!

daler added a commit that referenced this pull request Oct 11, 2017

Update bulk (#6274)
* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* Update picard to 2.13 (#6212)

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

daler added a commit that referenced this pull request Oct 11, 2017

Bioconductor 3.5 build bumps (#6203)
* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* add easy build version bumps

* run diff to origin/bulk

* fix line wraps, build numbers reset to 0, and template bioc version

* version bumps for relatively simple packages

* data packages

remove existing build.sh from recipes; add post-link.sh. A handful have
already been created, so their build numbers were not bumped.

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* first round of non-straightforward recipes

e.g., libgcc, skipped on osx, readline deps

* dexseq

maintain custom build script; no version change so reset to build: 0

* Update picard to 2.13 (#6212)

* dirichletmultinomial updates

ensure custom GSL, blas, gcc etc make it into recipe

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* dnacopy update

prev recipe listed gcc as build dep; changed it to the standard
linux/osx build deps.

* dose, and new dependency fgsea

prev version of DOSE had gmp listed as run and build deps, so retaining
it here

* ebimage update

orig recipe skipped osx; try not skipping for now

* flowcore update

retain custom parts of build script

* flowworkspace update

No version change, so build number set to 0. Build deps included
autoconf/automake for some reason, but gcc was not included. I kept
autoconf in there for now, and added gcc. Note that many of the deps
changes are just sort order.

* genefilter update

prev recipe included gcc, so keeping it here. No version bump, so build
number kept at 0.

* genomation updates

prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any
more. Keeping it (and the custom osx lines in build.sh) just in case.

* geoquery build.sh

must have missed this in a prev commit

* gosemsim update

new version no longer depends on r-rcpp, but keeping it just in case

* ipo update

prev version was skipped for OSX, removing skip for now

* lsymphony update

prev recipe depended on gcc, retaining here

* methylkit update

keeping build number: 0; prev recipe had libgcc as dep

* monocle update

parsing DESCRIPTION has an empty dep; skipped for osx. Since this was
added relatively recently, pretty sure it should stay skipped.

* fetch remote branch for diffs

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* comment out custom build.sh lines and meta.yaml deps

* comment out custom gmp dep

* comment out custom build.sh lines

* comment out automake build dep

* comment out previous genomation build.sh lines and r-rcpp

* gosemsim: comment out prev r-rcpp

* lpsymphony: comment out prev gcc

* comment out patch for methylkit

* comment out monocle skip for osx

* deseq2 update

comment out deps that are not listed in DESCRIPTION

* mosaics update

comment out prev version's libgcc run dep

* motifbreakr update

comment out osx skip

* motiv updates

comment out custom build.sh lines and deps

* mzr: comment out custom build deps and osx skip

* ncdfflow: comment out prev custom deps

* oligo: comment out previous extra deps, add separate build script

* oligoclasses update

comment out custom deps from prev recipe

* update pcamethods

* pchicdata update to make it a proper data package recipe

* phyloseq: comment out prev gmp dep

* piano update

comment out previous libgcc/llvm

* qdnaseq update: rm extra `r-` dep from empty DESCRIPTION entry

* rcas update

rm "r-" dep from empty DESCRIPTION

* rgalaxy update: rm "r-" empty dep

* rgraphviz: comment out prev patch and gcc

* rhdf5 update: comment out osx patch and gcc

* rhtslib update: comment out patches, gcc, and custom build.sh line

* risa update: comment out readline dep; reset build to 0

* rtracklayer update: fix dep version numbers which had "-" in them

* scan.upc update

keep build number at 0; comment out prev r-rsqlite dep and osx skip

* shortread: comment out custom build lines

* signer update: comment out build lines and prev deps

* sva update: comment out prev deps

* systempiper: comment out prev osx skip

* add diffbind

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

* update and otherwise unify r recipes

bgruening added a commit that referenced this pull request Oct 27, 2017

bioconductor 3.5 (#6505)
* Update bulk (#6274)

* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* Update picard to 2.13 (#6212)

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

* Bioconductor 3.5 build bumps (#6203)

* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* add easy build version bumps

* run diff to origin/bulk

* fix line wraps, build numbers reset to 0, and template bioc version

* version bumps for relatively simple packages

* data packages

remove existing build.sh from recipes; add post-link.sh. A handful have
already been created, so their build numbers were not bumped.

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* first round of non-straightforward recipes

e.g., libgcc, skipped on osx, readline deps

* dexseq

maintain custom build script; no version change so reset to build: 0

* Update picard to 2.13 (#6212)

* dirichletmultinomial updates

ensure custom GSL, blas, gcc etc make it into recipe

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* dnacopy update

prev recipe listed gcc as build dep; changed it to the standard
linux/osx build deps.

* dose, and new dependency fgsea

prev version of DOSE had gmp listed as run and build deps, so retaining
it here

* ebimage update

orig recipe skipped osx; try not skipping for now

* flowcore update

retain custom parts of build script

* flowworkspace update

No version change, so build number set to 0. Build deps included
autoconf/automake for some reason, but gcc was not included. I kept
autoconf in there for now, and added gcc. Note that many of the deps
changes are just sort order.

* genefilter update

prev recipe included gcc, so keeping it here. No version bump, so build
number kept at 0.

* genomation updates

prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any
more. Keeping it (and the custom osx lines in build.sh) just in case.

* geoquery build.sh

must have missed this in a prev commit

* gosemsim update

new version no longer depends on r-rcpp, but keeping it just in case

* ipo update

prev version was skipped for OSX, removing skip for now

* lsymphony update

prev recipe depended on gcc, retaining here

* methylkit update

keeping build number: 0; prev recipe had libgcc as dep

* monocle update

parsing DESCRIPTION has an empty dep; skipped for osx. Since this was
added relatively recently, pretty sure it should stay skipped.

* fetch remote branch for diffs

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* comment out custom build.sh lines and meta.yaml deps

* comment out custom gmp dep

* comment out custom build.sh lines

* comment out automake build dep

* comment out previous genomation build.sh lines and r-rcpp

* gosemsim: comment out prev r-rcpp

* lpsymphony: comment out prev gcc

* comment out patch for methylkit

* comment out monocle skip for osx

* deseq2 update

comment out deps that are not listed in DESCRIPTION

* mosaics update

comment out prev version's libgcc run dep

* motifbreakr update

comment out osx skip

* motiv updates

comment out custom build.sh lines and deps

* mzr: comment out custom build deps and osx skip

* ncdfflow: comment out prev custom deps

* oligo: comment out previous extra deps, add separate build script

* oligoclasses update

comment out custom deps from prev recipe

* update pcamethods

* pchicdata update to make it a proper data package recipe

* phyloseq: comment out prev gmp dep

* piano update

comment out previous libgcc/llvm

* qdnaseq update: rm extra `r-` dep from empty DESCRIPTION entry

* rcas update

rm "r-" dep from empty DESCRIPTION

* rgalaxy update: rm "r-" empty dep

* rgraphviz: comment out prev patch and gcc

* rhdf5 update: comment out osx patch and gcc

* rhtslib update: comment out patches, gcc, and custom build.sh line

* risa update: comment out readline dep; reset build to 0

* rtracklayer update: fix dep version numbers which had "-" in them

* scan.upc update

keep build number at 0; comment out prev r-rsqlite dep and osx skip

* shortread: comment out custom build lines

* signer update: comment out build lines and prev deps

* sva update: comment out prev deps

* systempiper: comment out prev osx skip

* add diffbind

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

* update and otherwise unify r recipes

* try removing r-base restrictions

* bioconductor-rhtslib additional deps

* rm r-base restriction on anything < 3.2.2

* rm a few more r-base restrictions

* a small round of bioconductor fixes

* try adding openblas

* bump ebimage version

* add bioconductor-matter

* rm r-base pin

* add zlibbioc dep to mzr

* add treeio

* re-enable libglu dep for r-mixomics

* add r-mqtl

* update s4vectors

* rm r restriction in biomformat

* fix ebiimage

* add libnetcdf dep to mzr

* rm r-base restriction for causalr

* update biocgenerics to try fixing s4vectors

* bump iranges

* add bioconductor-msnbase

* gcc for osx for fortran

* gcc for osx for fortran

* try libgfortran to get rhtslib to compile

* r-impute -> bioconductor-impute

* bump genomeinfodb

* assorted fixes

* assorted fixes 2

* assorted fixes 3

* assorted fixes 4

* assorted fixes 5

* try to fix shortread

* readd bioc-graph patch

* assorted fixes 6

* assorted fixes 7

* assorted fixes 8

* rebuild gosemsim

* add llvm for motiv and synergyfinder

* update rpath patches for rhdf5 and rgraphviz

* fix for bioconductor-dose

* try gcc for motiv?

* gcc for rhdf5?

* fix r-latticeextra dependency

thanks to @nsoranzo for spotting!

* Update meta.yaml

* fix buildstring for motiv

* skipping remaining osx packages

* add bioconductor-masigpro dev version as subdir

bgruening added a commit that referenced this pull request Nov 17, 2017

merge in bulk (#6800)
* Update bulk (#6274)

* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* Update picard to 2.13 (#6212)

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

* Bioconductor 3.5 build bumps (#6203)

* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* add easy build version bumps

* run diff to origin/bulk

* fix line wraps, build numbers reset to 0, and template bioc version

* version bumps for relatively simple packages

* data packages

remove existing build.sh from recipes; add post-link.sh. A handful have
already been created, so their build numbers were not bumped.

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* first round of non-straightforward recipes

e.g., libgcc, skipped on osx, readline deps

* dexseq

maintain custom build script; no version change so reset to build: 0

* Update picard to 2.13 (#6212)

* dirichletmultinomial updates

ensure custom GSL, blas, gcc etc make it into recipe

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* dnacopy update

prev recipe listed gcc as build dep; changed it to the standard
linux/osx build deps.

* dose, and new dependency fgsea

prev version of DOSE had gmp listed as run and build deps, so retaining
it here

* ebimage update

orig recipe skipped osx; try not skipping for now

* flowcore update

retain custom parts of build script

* flowworkspace update

No version change, so build number set to 0. Build deps included
autoconf/automake for some reason, but gcc was not included. I kept
autoconf in there for now, and added gcc. Note that many of the deps
changes are just sort order.

* genefilter update

prev recipe included gcc, so keeping it here. No version bump, so build
number kept at 0.

* genomation updates

prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any
more. Keeping it (and the custom osx lines in build.sh) just in case.

* geoquery build.sh

must have missed this in a prev commit

* gosemsim update

new version no longer depends on r-rcpp, but keeping it just in case

* ipo update

prev version was skipped for OSX, removing skip for now

* lsymphony update

prev recipe depended on gcc, retaining here

* methylkit update

keeping build number: 0; prev recipe had libgcc as dep

* monocle update

parsing DESCRIPTION has an empty dep; skipped for osx. Since this was
added relatively recently, pretty sure it should stay skipped.

* fetch remote branch for diffs

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* comment out custom build.sh lines and meta.yaml deps

* comment out custom gmp dep

* comment out custom build.sh lines

* comment out automake build dep

* comment out previous genomation build.sh lines and r-rcpp

* gosemsim: comment out prev r-rcpp

* lpsymphony: comment out prev gcc

* comment out patch for methylkit

* comment out monocle skip for osx

* deseq2 update

comment out deps that are not listed in DESCRIPTION

* mosaics update

comment out prev version's libgcc run dep

* motifbreakr update

comment out osx skip

* motiv updates

comment out custom build.sh lines and deps

* mzr: comment out custom build deps and osx skip

* ncdfflow: comment out prev custom deps

* oligo: comment out previous extra deps, add separate build script

* oligoclasses update

comment out custom deps from prev recipe

* update pcamethods

* pchicdata update to make it a proper data package recipe

* phyloseq: comment out prev gmp dep

* piano update

comment out previous libgcc/llvm

* qdnaseq update: rm extra `r-` dep from empty DESCRIPTION entry

* rcas update

rm "r-" dep from empty DESCRIPTION

* rgalaxy update: rm "r-" empty dep

* rgraphviz: comment out prev patch and gcc

* rhdf5 update: comment out osx patch and gcc

* rhtslib update: comment out patches, gcc, and custom build.sh line

* risa update: comment out readline dep; reset build to 0

* rtracklayer update: fix dep version numbers which had "-" in them

* scan.upc update

keep build number at 0; comment out prev r-rsqlite dep and osx skip

* shortread: comment out custom build lines

* signer update: comment out build lines and prev deps

* sva update: comment out prev deps

* systempiper: comment out prev osx skip

* add diffbind

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

* update and otherwise unify r recipes

* try removing r-base restrictions

* bioconductor-rhtslib additional deps

* rm r-base restriction on anything < 3.2.2

* rm a few more r-base restrictions

* a small round of bioconductor fixes

* try adding openblas

* bump ebimage version

* add bioconductor-matter

* rm r-base pin

* add zlibbioc dep to mzr

* add treeio

* re-enable libglu dep for r-mixomics

* add r-mqtl

* update s4vectors

* rm r restriction in biomformat

* fix ebiimage

* add libnetcdf dep to mzr

* rm r-base restriction for causalr

* update biocgenerics to try fixing s4vectors

* bump iranges

* add bioconductor-msnbase

* gcc for osx for fortran

* gcc for osx for fortran

* try libgfortran to get rhtslib to compile

* r-impute -> bioconductor-impute

* bump genomeinfodb

* assorted fixes

* assorted fixes 2

* assorted fixes 3

* assorted fixes 4

* assorted fixes 5

* try to fix shortread

* readd bioc-graph patch

* assorted fixes 6

* assorted fixes 7

* assorted fixes 8

* rebuild gosemsim

* add llvm for motiv and synergyfinder

* update rpath patches for rhdf5 and rgraphviz

* fix for bioconductor-dose

* try gcc for motiv?

* gcc for rhdf5?

* fix r-latticeextra dependency

thanks to @nsoranzo for spotting!

* Update meta.yaml

* fix buildstring for motiv

* skipping remaining osx packages

* add bioconductor-masigpro dev version as subdir

* bioconductor 3.6 updates

* bioconductor 3.6 remaining updates

* update bioconductor-treeio

* add bioconductor-rcy3

* update rDGIdb and SWATH2stats

* fix biocparallel

* update complexheatmap

* update DelayedArray

* update edgeR

* temporarily skip osx for rhdf5 and dep

* update rGREAT and matter

* add r-bh as dep to flowcore

* rm post-link for jaspar2018

* update rols

* add bioconductor-singlecellexperiment

* add bioconductor-raggedexperiment

* bump phyloseq

* increase subdags for bulk branch

* update annotationhub

* bump total subdag count

* update go.db

* update orgdb pkgs

* add rhtslib as dep for methylkit

* update org.Cf.eg.db

* add zlibbioc as dep for mzr

* update PSICQUIC and scran

* bump Rnits and methylumi

* add r-ncdf4

* fix checksum

* new version

* add bioconductor-rhdf5lib

* add bioconductor-beachmat

* add r-rcpparmadillo

* increase version

* add bioconductor-rhdf5lib

* add boost back to mzR

* upgrade to new version

* add hdf5array

* upgrade

* add the two new deps

* add genemeta

* add missing dep

* fix link

* add missing deps

* add bioc-cytolib

* add rprotobuflib

* add missing deps

* add missing deps

* add additional deps

* add automake dep to rprotobuflib

* minor formatting

* update BioC 3.5 packages recently added to master to BioC 3.6

cc @cbrueffer

* add r-bh to chemminer

* add missing dep

* fix automake to version 1.14

* add protobuf

* fix autoconf

* fix automake

* round 2 of ucsc updates

* blacklist remaining bioconductor build failures

* back to a single subdag

* skip isomirs on osx

* try additional fixes

* fix rprotobuflib

* revert #6758

* whitespace

* whitespace test

* add nloptr dep to flowdensity

* whitespace

* revert whitespace

* whitespace

bgruening added a commit that referenced this pull request Nov 22, 2017

bulk ucsc updates (#6884)
* Update bulk (#6274)

* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* Update picard to 2.13 (#6212)

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (#6237)

Depend on bcftools instead of conflicting with it.

* Lordec (#6144)

* first commit

* test changes and add comments

* fix command line

* remove binary

* remove stderr redirection

* fix testin adding || true

* fix command line test

* add zlib to recipe

* Bump vsearch version and add .gz support (#6239)

* Update peddy to 0.3.1. (#6236)

* Update peddy to 0.3.1.

* Update dependencies.

* Work around API changes in networkx >=2.0.

* Remove running the unit tests as suggested by @daler.

This was running into trouble with the minimal docker containers.

* Samtools 0.1.x (#6200)

* samtools: add version 0.1.12 till 0.1.15 with one semi test

* samtools: resolving dependencies for new versions - i hope

* samtools: pin requirements and expand CFLAGS

* samtools: fix incorrect sha256 and change back to md5

* samtools: os dependend Makefile adjustment

* patch ViennaRNA 2.4.1 RNAlocmin (#5994)

* bump viennarna

* increment bn

* Enable RNAlocmin

* Bump KneadData to 0.6.1 (#6244)

* Augustus deps (#6242)

* use latest augustus

* use latest augustus

* fix augustus, maker and busco recipes

* typo...

* typo...

* bump build numbers

* some problem with tests

* pin zlib

* try to fix test case

* fix test

* bioconductor-limma - add statmod as dependency (#6247)

* bioconductor-limma - add statmod as dependency

* bioconductor-limma - update build number

* Update meta.yaml

* VEP: bumped subversion (#6249)

* Cyvcf 0.8.0 (#6251)

* Preserve CyVCF 0.7.2.

* Update CyVCF to 0.8.0.

* Update IRFinder to 1.2.3. (#6252)

* Gecode 5.1.0 (#6253)

* Preserve Gecode 5.0.0.

* Update Gecode to 5.1.0.

* Genehunter-Modscore v3.1 (#6248)

* genehunter recipe
* skip osx

* Gmap 2017 09 30 (#6255)

* Preserve GMAP 2017.05.08.

* Update GMAP to 2017.09.30.

* Bump mashtree to 0.25 (#6258)

* Update Oncofuse to 1.1.1. (#6259)

* Freebayes seems to need libbz2 (#6260)

* Freebayes seems to need libbz2

* Pin zlib and bzip2

* Update meta.yaml

* Peptide shaker 1.16.14 (#6261)

* Preserve peptide-shaker 1.16.13.

* Update PeptideShaker to 1.16.14.

* Omero 5.4.0 (#6256)

* Bump OMERO recipe to version 5.3.4

- Bump version number and SHA1
- Add range to the zero-ice dependency
- User HTTPS

* Add skip-lints

* Fix character

* Bump to OMERO.py 5.4.0

* Do not skip lint

* Update: mosdepth 0.1.9 (#6264)

Includes breaking changes relative to 0.1.8: bcbio/bcbio-nextgen#2094
Has fixes for changed install.sh: Fixes #6263

* Add conda for tgDist #BioCon2017 (#6257)

* Add conda for tgDist #BioCon2017

* Correct comments after pull request

* fix runtime dep

* add cmake as buld time dependency

* skip build on OSX

* some recipes has been update for character format (#6267)

* Lelievrey (#6266)

* Add the pyasp recipe

* Correction of the version

* Add the missing summary

* Update build.sh

* small fixes

* Snakemake 4.2.0 (#6270)

* Bioconductor 3.5 build bumps (#6203)

* new version of graphicsmagick with --enable-symbol-prefix option when building (#6120)

* add bioconductor v3.4 versions (#6124)

* update r-aroma* (#6126)

* create recipe for perl-types-standard (#6125)

* Create build.sh

* Create meta.yaml

* Create recipe for perl-bio-cigar (#6118)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* remove bioconductor-peca from blacklist (#6129)

* rebuild r-packages (#6128)

* Update meta.yaml (#6134)

* Add BamM package (#6133)

* Add bamm

* Update galaxy_sequence_utils to 1.1.1 (#6136)

*  updated recipe (#6138)

* add bioconductor-jaspar2014 (#6137)

* Haystack 0.5.2 (#6140)

*  updated recipe

*  updated recipe

* dr-disco v0.11.0 (#6142)

* Add several R and Bioconductor recipes (#5428)

* initial version of recipes

*  remove last lines

*  add missing dependencies

*  added missing dependencies

*  added recipe for r-sfsmisc

*  move r-recipes to conda-forge and remove empty lines in bioc recipes

*  remove recipes that have been already added since last push

*  remove r-sfsmisc

* Update gffread to 0.9.9. (#6146)

* Add recipe for bioconductor-scran (#6143)

* Initial recipe of bioconductor-scran

* Modified R dependency

* Updated cmv to version 1.0.6 (#6147)

* Hansel | Pinning attrs version (#6135)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Pinning version of attrs.

* Update trim_galore to 0.4.4. (#6148)

* Downgrade networkx dependency (#6094)

Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see ewels/MultiQC#561 and 
ewels/MultiQC#592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC.

* Updating Last (lastal) to v874 (#6141)

* updating to last 874

* switch for OSX specific compilation with new makefile

* adding 8 byte binaries (for large DBs using big RAM)

* Snakemake 4.1.0 (#6150)

* Update Bamm (#6156)

* bump gnu-getopt build (#6157)

gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge

* [WIP] add sis (#6055)

* [WIP] add sis init

* [wip] sis build passes local

* [WIP] added python req

* [WIP] changed build script

* Add package MentaLiST-0.1.2 (#5856)

* Initial commit

* Updated to v0.1.2

* Updated url and sha256 hash

* Filled in missing fn field

* Added requirement mpfr

* Specify openblas build to force conda-forge build of julia

* Revert last change

* Updated build section to skip osx build (no julia available)

* Moved MentaLiST.jl -> mentalist symbolic link command to build.sh

* Mapsembler2 (#6159)

* Remove unneeded samtools run requirement (#6155)

CrossMap uses pysam.

* update shovill (#6152)

* bumped shovill version to 0.8.0

* added conda_perl

* added version requirements

* discosnp (#6149)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* Haystack 0.5.2 (#6164)

*  updated recipe

*  updated recipe

* updated sha256

* Haystack 0.5.2 (#6165)


* updated sha256

* fixed build number

* Kissplice (#6154)

* Kissplice

* pin zlib against {{CONDA_ZLIB}}*

* add python libraries

* remove make test

* fix python dependency

* uncomment make test

* IntaRNA v2.0.5 (#6160)

* v2.0.5 released

* reset build number to 0

* Update: bcbio-vm for ansible 2.x compatibility (#6167)

* Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166)

* deeptools: add old 1.5.8.2 version

* deeptools: minor update for linux build

* deeptools: add missing requirement for ucsc-bedgraphtobigwig

* deeptools: add 1.5.9.1

* Perl io gzip (#6158)

* first commit

* first commit

* Remove zlib-devel dependency

* Add a dependency to zlib (zlib-devel not found)

* Update build.sh with CFLAGS and LDFLAGS

* update build.sh with CFLAGS and LDFLAGS

* Add zlib reuirement

* Back to the perl-io-html model

* Back to the perl-io-html model + env vars for compliation and ld

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* [lint skip uses_setuptools for recipes/qcumber]

* pin zlib

* bump build number (#6174)

* Added recipe for bioconductor-copynumber (#6170)

* Haystack 0.5.2 (#6176)

*  updated recipe

*  updated recipe

* updated sha256

* fixed build number

* updated hash

* improved patch (#6173)

* Update meta.yaml (#6179)

Oups, I forgot to check the build number

* Update Bamm (#6180)

* Discosnp fix dependencies (#6182)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* Bump mash to 2.0 (#6168)

* Bump mash to 2.0

* Pin zlib

* Discosnp fix scripts path in .sh (#6185)

* discosnp

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* fix dependencies binaries not found during the execution

* fix scripts path in .sh

* fix dbh5 path for copy

* Update mssttitch version to 2.5 (#6181)

* Update mssttitch version to 2.5

* Fix setup.py for conda after linting

* GraphProt (#6183)

* add GraphProt version 1.1.6

* update shiver (#6175)

* update Graphprot version 1.1.7 (#6188)

* add python3 dependency, need at least weblogo 3

* version bump

* Tantan (#6189)

Adding tantan: a utility for masking low complexity sequences

* Updated haystack sha256 (#6178)


* updated sha256

* updated sha256

* Haystack bio (#6190)

* updated haystack 0.5.3

* updated haystack 0.5.3

* updated sha256

* updated sha256

* updated sha256

* updated sha256

* updated last aligner to 876 (#6191)

* updated last aligner to 876

* updated spades to 3.11.1 bug-fix release (#6192)

* updated sha256sum (#6193)

* adding mappy (#6195)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse (#6196)

* adding mappy

* adding import test

* removed double whitelines

* fixing yaml

* fixing yaml - adding build

* fixing yaml - removed space

* fixing yaml - no idea

* fixed files - maybe

* added zlib

* dummy change

* trying environmental variables in build.sh

* removed comments

* specified CONDA zlib in requirements

* adding nanolyse

* lowercase name

* corrected import test

* Fix url and description (#6197)

* Update vcf2db to 2017.09.14. (#5433)

* Bumped STAR-Fusion version (#6198)

* HUMAnN2 requires diamond<0.9.0 (#6194)

* HUMAnN2 requires diamond<0.9.0

* Fix pre-existing linting errors

* Increment build numbers

* update r-sartools (#6201)

* add easy build version bumps

* run diff to origin/bulk

* fix line wraps, build numbers reset to 0, and template bioc version

* version bumps for relatively simple packages

* data packages

remove existing build.sh from recipes; add post-link.sh. A handful have
already been created, so their build numbers were not bumped.

* Update: latest version with CollectErccMetrics (#6205)

* Takeabreak software (#6145)

* first commit for takeabreak

* add zlib requirement

* fix sed compatibility

* pin zlib against {{CONDA_ZLIB}}*

* delete decrease of memory

* Mapsembler2 (#6206)

* Mapsembler2

* fi mapsembler2 deps

* Htseq 0.9.1 (#6204)

* Add recipe for HTSeq-0.9.1

* Delete files

* Add recipe for htseq

* Update vsearch to 2.4.4 (#6211)

* first round of non-straightforward recipes

e.g., libgcc, skipped on osx, readline deps

* dexseq

maintain custom build script; no version change so reset to build: 0

* Update picard to 2.13 (#6212)

* dirichletmultinomial updates

ensure custom GSL, blas, gcc etc make it into recipe

* bump to 0.8.1 (#6058)

* bump to 0.8.1

* change patch file to reflect updated code

* add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code

* dnacopy update

prev recipe listed gcc as build dep; changed it to the standard
linux/osx build deps.

* dose, and new dependency fgsea

prev version of DOSE had gmp listed as run and build deps, so retaining
it here

* ebimage update

orig recipe skipped osx; try not skipping for now

* flowcore update

retain custom parts of build script

* flowworkspace update

No version change, so build number set to 0. Build deps included
autoconf/automake for some reason, but gcc was not included. I kept
autoconf in there for now, and added gcc. Note that many of the deps
changes are just sort order.

* genefilter update

prev recipe included gcc, so keeping it here. No version bump, so build
number kept at 0.

* genomation updates

prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any
more. Keeping it (and the custom osx lines in build.sh) just in case.

* geoquery build.sh

must have missed this in a prev commit

* gosemsim update

new version no longer depends on r-rcpp, but keeping it just in case

* ipo update

prev version was skipped for OSX, removing skip for now

* lsymphony update

prev recipe depended on gcc, retaining here

* methylkit update

keeping build number: 0; prev recipe had libgcc as dep

* monocle update

parsing DESCRIPTION has an empty dep; skipped for osx. Since this was
added relatively recently, pretty sure it should stay skipped.

* fetch remote branch for diffs

* Add recipe for hicrep by Tao Yang. (#6213)

* Explicit set of LGPL license (#6210)

* Explicit set of LGPL license and move license link to license_file meta field

* refer license_file to source directory

* set explicit license instead of reference to LICENSE source file (#6208)

* set explicit license instead of reference to LICENSE source file

* add license_file info

* update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214)

* Flexbar 2.5.0 (#6187)

* initial commit

* move to separate dir and start 3.0.2 version

* prepare version 3.0.3

* dont do 303

* enable osx and pin bzip2 and zlib

* unpin bzip2

* have to create documentation directory

* remove libgcc build dep

* Add yanagiba (#6217)

* Add yanagiba

* Fix url

* Remove duplicated dep

* Skip py27

* update Graphprot tests to run in docker setup (#6218)

* add python3 dependency, need at least weblogo 3

* version bump

* remove libgcc runtime tep

* see if libcxx is required at all

* directly get test files from github

* fix tests for wget download of test files

* add wget runtime dependency for downloading testing data within docker

* remove explicit python stuff, depends implicitely on python via weblogo

* clean up test calls again

* use curl instead of wget

* Update bcftools to v1.6 (#6221)

* [update] pyquant-ms to 0.2.1 (#6222)

* Update version

* Skip python 3 build

* Commet recipe (#6220)

* add commet recipe

* add python dependency :)

* Fix invalid license link (#6209)

* Fix invalid license link

Explicit set of license and add correct link to license file on github

* add skip-lints as source uses only git_url, upstream not providing tags or archives

* refer to license in source code instead of github link

* use archive instead of git_url

* increase build number to force new release update

after modification of source url instead of git_url, increatse build number to get a new fresh built

* fix license file location

* Create recipe for rad_haplotyper (#6202)

* Create build.sh

* Create meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update snpEff, SnpSift to 4.3.1r. (#6224)

* Update SnpSift to 4.3.1r.

* Update snpEff to 4.3.1r.

* Pairix 0.3.0 (#6223)

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* update sequana to version 0.5.2 (#6226)

* Ped parser 1.6.6 (#6229)

* Save ped_parser 1.6.5.

* Update ped_parser to 1.6.6.

* Fix LINT check setup_py_install_args.

* Update htsbox to r340. (#6230)

* ViennaRNA 2.4.1 (#6228)

* build.sh of v2.3.5

* meta.yaml of v2.3.5

* tutorial build disabled

* v2.4.1 enabled

* summary tag indention

* RNAlocmin disabled since not compiling

* canu 1.6 (#6216)

* canu 1.6

* set machine requirements

* fix

* remove the second test

* Sift4g recipe (#6227)

* Add recipe for HTSeq-0.9.1

* Add recipe for sift4g

* Updating Hansel to version 0.2.0 (#6225)

* Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file.

* Fixing the directory within build.sh

* Fixing the ordering of the sed command, moving to after the pip install.

* Removing SED tailoring for now, and adding "which" as a test command.

* Changing repository as we have now migrated to the PHAC NML repository.

* Changing to official release branch now.

* Fixing MD5 value.

* Fixing requirements and test command.

* Changing the testing command, as the new help contains invalid characters.

* Removing list of authors from summary within meta.yaml.

* Adding Detailed Summary

Added detailed summary including authors.

* Deleting python version file.

Deleting un-needed file.

* Changing recipe to rely on PyPi and fixed the build script.

* Adding python setup parameters.

* Removing pinning, and adding skip for Python 2.

* Changing URL to standard. Added variable for hash type and val.

* Bumping version of bio_hansel to 0.2.0

* Fixing - to _

* add cassiopee index/search sequence tool (#6215)

* add cassiopee index/search sequence tool

* pin boost version

* add boost related libraries as requirements though should be done by boost

* try setting boost options on cmake for linux/travis case

* add debug info to find why boost does not find deps

* add LDFLAG to PREFIX/lib

* add some C FLAGS for compilation to try to find missing deps

* pin bioconda dep libs and append xFLAGS instead of set

* Set hstlib version to use as recipe clone master branch (#6207)

* Set hstlib version to use as recipe clone master branch and does not compile anymore.
Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package.

Add hash to source.

* fix manpage copy for osx

* Update NucleoATAC to version 0.3.4 (#6177)

* Update NucleoATAC to version 0.3.4

Added imports test, which forces a build
Add fix for zlib.h not found
Preserve nucleoatac version 0.3.1

* Use template-vars for nucleoatac package info

* Cleaning up some test code

* Update vcf2maf to 1.6.14. (#6232)

* Commet apply patch (#6233)

* add commet recipe

* add python dependency :)

* patch commet to load dependencis correctly

* add build number

* Update biobambam to 2.0.78. (#6234)

* Update galaxy_sequence_utils to 1.1.2 (#6235)

* Recipes for R packages alakazam and prestor. (#6199)

* Recipes for R packages alakazam and prestor.

* Added missing dependencies.

* Removed #win specific things and updated gcc/llvm dependencies.

* Anvio to versino 3 (#6238)

* moving to anvio 3
* adding centrifuge as a run dependency

* bowtie2 2.3.3.1 (#6241)

* Update gffcompare to 0.10.1. (#6243)

* Update bcftools-snvphyl-plugin to 1.6 (