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Update EMA to v0.6.2 #10141

Merged
merged 1 commit into from Jul 30, 2018
Merged

Update EMA to v0.6.2 #10141

merged 1 commit into from Jul 30, 2018

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arshajii
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  • 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).

@arshajii arshajii merged commit 6cccf71 into bioconda:master Jul 30, 2018
@arshajii arshajii deleted the ema branch July 30, 2018 18:35
asmariyaz23 pushed a commit that referenced this pull request Aug 14, 2018
@brianjohnhaas @asmariyaz23
Trinity (#10419)
3df4ccc 
* add convert_zero_one_based (#10001)

* add convert_zero_one_based
* remove unecessary tests
* test import

* Gembs (#10109)

* gembs: passes a mulled build
* correcting dependencies
* gembs: passes a mulled build
* correcting dependencies
* pointing to the current gem3-mapper instead of a custom version
* removing openssl
* gembs: passes a mulled build
* correcting dependencies
* pointing to the current gem3-mapper instead of a custom version
* removing openssl
* starting build at 0
* Changing to the main repository instead of the testing fork

* Update sevenbridges-python recipe to 0.15.0 (#10113)

* update to new version (#10015)

* update to new version

the old version had a bug whereby some reads were dropped. See mourisl/Rcorrector#12

* remove recipe from blacklist

* Update meta.yaml

* try adding flags

per comment from @jpuritz

* fix makefile

* bump for alevin hotfix (#10118)

* bump for alevin hotfix

* Update meta.yaml

Put md5sum for the zip, not .tar.gz.  Correct that.

* Bump JBrowse version to 1.15.0 (#10116)

Add missing dependency perl-io-uncompress-gunzip.

Support osx.

* Update krocus to v0.2.3 (#10115)

*  updating to ragout v2.1, should fix the problem with inconsistent ... (#10105)

* updating to ragout v2.1, should fix the problem with inconsistent newick package versions

* Dialign2 (#10098)

* Started work on dialign2

* Fixing build/host

* compiler

* still compiler error

* still

* still working on compiler

* should be fixed

* Fixed typo

* desperate measures

* typo

* whatever

* Update meta.yaml

* fix hash

* freaky circleci, please run

* working on paths and exports

* still working on paths and exports

* still working on paths

* last fixes

* verylast fixes

* verylast fixes?

* wtf circleci

* wtf circleci aber echt

* Fixing license

* Working

* env vars export

* Working on postlink

* Working on prelink

* Working on env vars

* Done?

* skipping osx and done i hope

* Added pre-unlink and added DOI

* Fixing exports

* Removed unnecessary scripts, added wrapper

* Added patch and sed workaround for env var DIALIGN2_DIR

* Fixing sed command

* Fixing sed command again

* I hate sed

* fixed typo and eyecandy

* Remove various packages from the blacklist (#10117)

* Remove various packages from the blacklist

* eqtlbma needs to always have openblas included

* Patch mamotif so it uses matplotlib.use('Agg') early on

* Skip eqtlbma on OSX due to openmp

* Add r-bipartite (#10119)

* Add r-bipartite

* removed 2nd url

* Add r-phylomeasures (#10120)

* Add r-phylomeasures

* removed 2nd url

* Bump perl-file-path (#10123)

* Bump perl-file-path

* Small fixes

* Fix 2 perl packages (#10124)

* bump pysam (#10126)

* Update primer3 to v2.4.0 (#10122)

* Update primer3 to v2.4.0

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

Bump primer3 to `v2.4.0`.

* Review fixups for Update primer3 to v2.4.0

* R phylosignal (#10128)

* Add r-phylosignal

* Removed fn:

* removed all win

* fixed meta.yaml; ade4 now updated to 1.7_11

* R coenocliner (#10127)

* Add r-coenocliner

* modified maintainers

* add msisensor (#10092)

* add msisensor

* skip macos

* change include and lib

* fix ncurse

* add tinfo

* add cpath

* add LIBRARY_PATH

* Update to fastp v0.19.3 (#10131)

This version provides a fix for possible deadlock on cloud-based docker env.

* Add r-ggrasp (#10129)

* Add r-ggrasp

* trivial change to restart checks now the r-bgmm is on conda-forge

* updated r-nodiv recipe; unblacklisted (#10132)

* Blood moon blaclist changes (#10133)

* remove a few things from the blacklist

* Try something for osx

* skip xatlas on osx

* Fix two more perl (#10135)

* Fix perl-image-size

* Fix perl-aceperl

* Add perl-cache-cache

* Add perl-ipc-sharelite

* Add perl-digest-sha1

* bumping to 0.7.1 (#10136)

* Remove packages from the blacklist (#10134)

* Remove packages from the blacklist

* Fix fermi on osx I hope

* Ah, only gnu assumes inline functions are static

* preseq 2.0.3 includes the wrong header for proper building on newer OSX versions. Try to cxxflags around this.

* Skip preseq on OSX, clang doesn't like the older headers

* Added recipe prototype for pymisc-utils (#10139)

* Added recipe prototype for pymisc-utils

* Updated build dependencies

* Updated repo url

* Fixed copying of executables

* Added dependency

* Minor fix

* Skip python 2

* Idr (#10112)

* idr: push version to 2.0.4.2

* OMERO.py 5.4.7 (#10138)

* OMERO.py 5.4.7

* Bump version in setup.py to 5.4.7

* Update EMA to v0.6.2 (#10141)

* Add r-htssip (#10121)

* Add r-htssip

* converted r- to bioconductor-

* trivial change to restart checks

* Ragout 2.1.1 (#10144)

* ragout 2.1.1 update (now as a Python package)

* Riboseed updates (#10143)

* [wip] riboseed add quast and networkx

* update build number

* bump version, remove dep on pyutilsnrw

* [wip]  remove quast (single tear), which isn't built for py3 on conda

* bump version

* bump version to fix cmdline args

* updating cromwell to 0.34 (#10145)

* updating cromwell to 0.34

* gembs, rebuild (#10140)

removing restrictions on python beyond build-skip. matplotlib not needed for building

* PacBio: bump lima to 1.7.0 (#10151)

* gembs: adding missing runtime dependencies and moving build script to meta file (#10150)

* Jcvi python module (#10152)

* add jcvi recipe

* fixes

* update biokit to v0.4.4 (#10148)

* update biokit to v0.4.4

* Jcvi is python 2 only (#10153)

* jcvi is python 2 only

* negation bug in my head

* changed to 1.0.6 (#10157)

* updated bbmap to 38.16 (#10159)

* forgi: loosened the dependencies (#10156)

* Grid6 (#10158)

* changed to 1.0.6

* changed to veersion 1.0.6

* Update biohansel to v2.1.0 (#10160)

* Update biohansel to v2.1.0

* Python 3.6 builds only

* Update meta.yaml

* Fixing perl-json-xs and deps (#10161)

* Fix perl-common-sense

* Fix perl-types-serialiser

* Bump perl-canary-stability

* Bump perl-json-xs

* Unblacklist

* Small fixes

* Build perl-json-xs later

* Unblacklist perl-json-xs (#10163)

* PIPITS 2.2 update. (#10164)

* Perl OS X fixes 20180731 (#10165)

* Various perl OS X fixes.

* Remove perl-parallel-forkmanager from blacklist.

* Riboseed updates (#10162)

* [wip] riboseed add quast and networkx

* update build number

* bump version, remove dep on pyutilsnrw

* [wip]  remove quast (single tear), which isn't built for py3 on conda

* bump version

* bump version to fix cmdline args

* bump version

* Update meta.yaml

* Unblacklist 2 more perl  (#10166)

* Unblacklist 2 perl

* Unblacklisting

* Fix typo

* alfred v0.1.8 (#10168)

* bump build numbers for htslib dependent recipes.

* PacBio: Update `pbcommand` to 1.1.1 (#10172)

* PacBio: Update `pbcore` to 1.5.1 (#10173)

* Remove obsolete build script.

* PacBio: Remove `pbcommand` from build-fail-blacklist (#10176)

* PacBio: Initial addition of `pbcoretools` (#10169)

* bump htslib to get libdeflate pinning

* 2.1.3 update (#10180)

* updated bbmap to 38.18 (#10178)

* snakemake 5.2.2 (#10179)

* snakemake 5.2.2

* add python as run dependency.

* Chado tools (#9991)

* bioconda recipe for chado-tools
* use meta.yaml created by skeleton
* set source to github
* remove build script section
* remove import section
* restore import section
* correction
* noarch: python

* Update mob_suite to 1.4.6 (#10088)

* Update mob_suite to 1.4.6
* Update sha256

* added recipe for itsxpress 1.6.4 (#10099)

* Enable python3.6 build (#10101)

This recipe should not skip py36, as version 4.0.3 of RGI primarily supports Python3. This change will enable rgi to work in Python3 environments.

* bump phyluce to 1.6.6 (#10114)

* bump phyluce to 1.6.6
* adding DOI

* Update breseq to v0.33.0 (#10175)

* Update breseq to v0.33.0

* add disable-compiler-version-check.patch

* Update meta.yaml

* Dropseq tools (#10170)

* first attempt

* package name now lowercase

* test command gave an exit 1

* another try

* try..

* missed a slash

* wrong test to test

* qutoe

* finalizing recipe before push

* last test

* add a test on help

* added test for each command

* Add deepsvr (#10167)

* add deepsvr

* switch install to pip

* test cli entry point in build

* update sha

* update sha

* update sha

* Test help command

* Remove command test

* Add command test

* Perl OS X fixes 20180801 (#10184)

* More perl fixes for OS X.

* Remove unneeded dependency.

* Update schema-salad to 2.7.20180731120629 (#10195)

* Update gatk4 to 4.0.7.0 (#10191)

* Update toulligqc to v0.10 (#10192)

* Update gridss to v1.8.0 (#10193)

* Update dxpy to v0.257.3 (#10197)

* Update anndata to 0.6.6 (#10186)

* Update anndata to 0.6.6

* python >=3

* require python >=3.5

* Update isatools to v0.10.2 (#10190)

* Update chado-tools to v0.0.4 (#10189)

* enabled jni; bumped version to 38.19 . (#10185)

* enabled jni; bumped version to 38.19 .

* construct test file on the fly

* use already-installed resource file for testing

* added nodisk to avoid creating leftover files after test

* changed tests to what blast does

* fixed filenames

* another filename fix

* dropped pipefail

* Update mglex to v0.2.1 (#10188)

* Update mglex to v0.2.1

* update meta.yaml

* New: wes-service client only (#10200)

Provides a client for Workflow Execution Service (WES) endpoints,
part of the GA4GH initiative.

* Riboseed updates (#10202)

* [wip] riboseed add quast and networkx

* update build number

* bump version, remove dep on pyutilsnrw

* [wip]  remove quast (single tear), which isn't built for py3 on conda

* bump version

* bump version to fix cmdline args

* bump version

* bump version

* 2.1.4 release (#10204)

* trigger rebuild

* Trinotate: fix error in Build_Trinotate_Boilerplate_SQLite_db.pl (#10205)

* fix path error in Build_Trinotate_Boilerplate_SQLite_db.pl

* patch trinotate_report_summary.pl too

* Move PyVCF to conda-forge (#9979)

* Add recipe for hotspot3d 0.6.0. (#10209)

* Fasttreecondbuild3 (#10177)

* remove FastMP test

* add SRC_DIR and filename to build script and move MP into linux-specific build

* remove fasttree from blacklist

* update older versions as well

* trigger rebuild

* bump build versions

* change the tests so that they end

* Update WGCNA to 1.63 (#10203)

* phantompeakqualtools first commit (#10171)

* phantompeakqualtools first commit

* add in r-spp dependency

* correcting dependencies

* Updated ont-tombo to version 1.4. (#10182)

* Updated ont-tombo to version 1.4.

* Removed setuptools from run requirements.

* Added extra identifier to the bioarxiv pre-print.

* Update meta.yaml

* Update pycoqc to 1.1.alpha3 (#10198)

* Update pycoqc to 1.1.alpha3

* add noarch: python

* remove universal binaries for ViennaRNA (#10043)

* remove universal binaries for ViennaRNA

* the flag in configure causes a 1.33-2.00x slowdown (docs say it
interferes with some link-time optimizations)
* the flag is unnecessary since its intent was to bind with Apple's
stock python distribution (rather than conda)

echo 'GCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA' | time RNAcofold --noPS -p

RNAcofold --noPS -p  0.02s user 0.00s system 89% cpu 0.030 total

RNAcofold --noPS -p  0.01s user 0.00s system 74% cpu 0.022 tota

* bump buildno to trigger build

* Bump libsequence to 1.9.4.  Update dependencies, which are build-only! (#10210)

* Bump libsequence to 1.9.4.  Update dependencies, which are build-only!
Compiler and run unit tests after build.

* skip os x for now.  the case-sensitivity of the file system makes building impossible until we get closer to libseq 2.0

* Unblacklist perl-file-find-rule (#10218)

* unblacklist perl-file-find-rule

* workaround from conda/conda-build#2824

* Fix python dependency for Stacks 2.1 and remove Stacks dependency from dDocent (#10213)

* remove python spec

* remove python

* remove python

* remove stacks dependency from dDocent

* Update meta.yaml

* Add deepbinner. (#10111)

* Add deepbinner.

* overwrite numpy pinning because tensorflow needs a newer version.

* rebuild htslib in the hope that libdeflate pinning is now included on linux as well.

* add suport for centroid rna package (#9647)

* add suport for centroid rna package

* add suport for centroid rna package

* linting fail - fix by removing fn name

* Change test from python to sh script.

* Change test from python to sh script.

* skiping osx, reintroducing python based test (simple check of output code not reliable)

* add doi identifiers

doi iderntifiers directly related to programs contained in package

* run test from meta with grep instead of run_test.py


add py2k to skip

per request adding py2k to skip

* suppress output of the test commands

* unblacklist perl-dbi (#10236)

* unblacklist perl-dbi

* permission problem with fix_shebang

* chmod again

* Update r-wgcna build

* Update build number

* Fix macs2 recipe (#10232)

* New recipe: Slamdunk (#10199)

* Slamdunk recipe setup.

* No fixed java version.

* Java-jdk -> Openjdk.

* PREFIX removed from recipe.

* wget dependency added.

* conda build checking.

* path extensions.

* Only py2.7 requirement.

* Win skip removed.

* lka

* lkal

* pip install switch

* samtools dependencies added

* senf

* senf1

* recent

* satool

* sha

* shaupdate

* freaky

* testy

* testz

* Slamdunk v0.3.1 bioconda build 0.

* SHA256 updated.

* Skipping py3 build. Using pip.

* Python3 builds not skipped - otherwise package will not be built at all.

* OSX build deactivated.

* Skip py3k. OSX activated.

* OSX deactivated for good.

* .buildkite restored. Skip merged into one-liner.

* Unblacklist perl-dbd-sqlite (#10239)

* Unblacklist perl-dbd-sqlite

* permission problem

* Update treetime to v0.4.1 (#10229)

* Update nglview to v1.1.5 (#10217)

* Unblacklist trinotate recipe (#10206)

* unblacklist trinotate

* this module needs to be rebuilt

* fix broken recipe

* fix find command

* rebuild

* permission problem

* Update build.sh

* python-chado 2.1.5 (#10246)

* Add recipe for connectome-workbench 1.3.1. (#10248)

* Add recipe for connectome-workbench 1.3.1.

* Use extended container.

* Update: wes-service-client, bcbio-variation-recall, bcbio (#10249)

- bcbio-variation-recall: Avoid use of gatk-framework. Fixes bcbio/bcbio-nextgen#2412
- wes-service-client: python2/3 fixes
- bcbio: RNA-seq CWL improvements

* Support osx. (#10251)

zlib not needed.

* Change compiler from c to cxx and bump build number. (#9900)

* Change compiler from c to cxx and bump build number.

* fix older recipes and remove fwdpp from blacklist

* reset build number

* blacklist old versions of fwdpp

* remove fwdpy11 from blacklist

* bump fwdpp to 0.6.1

* try not defining any environment variables related to compilation

* pull build fail blacklist from master

* include C compiler, too

* Update vt to 0.57721 (#10253)

* Trimmomatic update (#10257)

* update trimmomatic

* Update and rename trimmomatic.sh to trimmomatic.py

* Update build.sh

* Update meta.yaml

* Update trimmomatic.py

* remove old trimmomatic pkg

* Pairtools v0.2.0 (#10252)

* pairtools v0.2.0

* MultiQC version 1.6 release (#10254)

* MultiQC version 1.6 release

* Update meta.yaml

* Update meta.yaml

* bump version (#10258)

* adding recipe for lordfast (#10255)

* adding recipe lordfast

* adding c++ compiler

* Perl fix 11 (#10259)

* Bump perl-array-compare

* Fix perl-unicode-map

* Unblacklist

* Perl fix 12 (#10261)

* Add perl-module-loaded

* Add perl-graphics-colornames

* Fix perl-graphics-colorobject

* skesa 2.2-2 (#10262)

* Update shovill to 1.0.0 (#10256)

* Fastqe (#10245)

* Add fastqe

* Fix whitespace in description and noarch lint skip [lint skip should_be_noarch for recipes/fastqe]

* Add GeneNoteBook recipe (#10089)

* genenotebook recipe

* Build from prebundled tarball

* Bump perl-gd and add new dependency (#10260)

* Add perl-test-fork

* Bump perl-gd

* Revert extra deps

* NovaSplice (#10250)

* attempt #1 to add novasplice recipe

* novasplice

* Update meta.yaml

* Perl fix 13 (#10265)

* Bump perl-file-fetch

* Bump perl-file-sharedir-install

* Bump perl-file-sharedir

* Bump perl-html-tree

* Unblacklist

* Build perl-file-sharedir later

* Unblacklist perl-file-sharedir (#10267)

* Perl fix 14 (#10266)

* Add perl-padwalker

* Add perl-devel-cycle/

* Add perl-test-memory-cycle

* Fix perl-font-ttf

* Unblacklist

* Correct build numbe

* Correct build numbe

* Unblacklist perl-pdf-api2 (#10268)

* Fix perl-pdf-api2

* Unblacklist

* Remove various packages from the blacklist (#10269)

* Remove various packages from the blacklist

* graphmap uses openmp, which is problematic with clang

* Update bpipe to 0.9.9.6 (#10240)

* Update bpipe to 0.9.9.6

* Update meta.yaml

* add new commit to retrigger test

* use http instead of ftp (friendlier with travis) (#10272)

* gmap 2014.12.28 (#10181)

* gmap 2014.12.28

* added host section

* Update meta.yaml

* Add -ldeflate to gqt compile command. Add missing limit macro defintion to pindel compile command.

* Update: bcbio, bcbio-vm with WES support (#10274)

* ensure SIZE_MAX is defined.

* Fix flags.

* try setting variable as make argument

* set generic flags.

* Update sleuth to 0.30.0. (#10278)

* upgrade rscape (#10208)

* upgrade rscape

* glib

* clean then compile

* Update meta.yaml

* debug info

* relax plot version

* simplify test

* minor fix

* older versions

* older test

* even older

* even older

* no clean

* orig test

* bump version

* grep test

* working version

* bump working version

* Create conda_build_config.yaml

* clean then build

* v0.7.3

* upgrade rscape

* glib

* clean then compile

* Update meta.yaml

* debug info

* relax plot version

* simplify test

* minor fix

* older versions

* older test

* even older

* even older

* no clean

* orig test

* bump version

* grep test

* working version

* bump working version

* Create conda_build_config.yaml

* clean then build

* v0.7.3

* Update conda_build_config.yaml

* fix R2R makefile

* gxx config

* minor cleanup

* skip mac

* rnachipintegrator 1.1.0 (#10276)

* rnachipintegrator: update to version 1.1.0.

* Update meta.yaml

* Dialign fix, again (#10279)

* Fixing patch

* Increased build number

* Delete patchdialign.txt

* Clinker (#10244)

* Add clinker with wrapper

* Add full test

* Remove test data test as per guidelines

* Updated minimap2 to v2.12 (#10282)

* delly: update to fix boost linker error (#10283)

Trying to fix:
```
delly: symbol lookup error: delly: undefined symbol: _ZN5boost15program_options3argE
```
and seems like it might need a re-build after being unblacklisted.

* Unblacklist a few perl packages (#10275)

* unblacklist a few perl packages

* add back to blacklist temporarily

* add back temporarily

* another one

* trigger new test

* mac permissions

* reset build number [ci skip]

* mac permissions

* try to rebuild mac packages maybe

* damn, typo

* mac perms

* trigger new test

* trigger new test

* trigger

* Update mlst to 2.11 (#10263)

* Remove various packages from the blacklist (#10280)

* Remove various packages from the blacklist

* Tepid gave a rather tepid response

* update gubbins to a new version (#10289)

* Slamdunk package fix (#10290)

* Slamdunk recipe setup.

* No fixed java version.

* Java-jdk -> Openjdk.

* PREFIX removed from recipe.

* wget dependency added.

* conda build checking.

* path extensions.

* Only py2.7 requirement.

* Win skip removed.

* lka

* lkal

* pip install switch

* samtools dependencies added

* senf

* senf1

* recent

* satool

* sha

* shaupdate

* freaky

* testy

* testz

* Slamdunk v0.3.1 bioconda build 0.

* SHA256 updated.

* Skipping py3 build. Using pip.

* Python3 builds not skipped - otherwise package will not be built at all.

* OSX build deactivated.

* Skip py3k. OSX activated.

* OSX deactivated for good.

* .buildkite restored. Skip merged into one-liner.

* slamdunk v0.3.1 -> slamdunk v0.3.2 (Softlink fix).

* Update confindr to v0.3.3 (#10224)

* Update confindr to v0.3.3

* Update meta.yaml

* Delete build.sh

* Adding recipe for XHMM (#10183)

* Remove strainest, starseqr, strudel, and svtools from the blacklist (#10291)

* Build number updated. sha256 updated. (#10292)

* updates bwameth to 0.2.2 (#10293)

* Add setuptools as run dependency (needed by some helper). Add python as a host dependency, to work around problems with the metapackage. (#10294)

* adding recipe for hulk (#10295)

* nextflow 0.31.1 (#10296)

* nextflow 0.31.1

* reset build number

* Perl fix 15 (#10298)

* Fix perl-forks

* Fix perl-acme-damn

* Unblacklist

* Remove a few more perl recipes from blacklist (#10287)

* remove a few more perl recipes from blacklist

* temp disable

* we need perl-cgi on mac

* tab

* mac fixes

* various mac fixes

* fix lint missing_tests

* test

* modified the wrong recipe

* some broken perl osx packages

* Needed by perl-soap-lite

* perl-xml-twig dep problem

* damn... forgot this

* add back to blacklist until next batch

* mac permission

* mac rebuild

* fix hang

* perm problem

* blacklist for now

* Perl fix 16 (#10301)

* bump perl-excel-writer-xlsx

* Bump perl-archive-zip

* Unblacklist

* Bump perl-graphviz (#10303)

* Bump perl-test-inter (#10306)

* NanoSim-H 1.1.0.4 (#10307)

* NanoSim-H 1.1.0.4

* Update sha256

* Reset build nb

* flye 2.3.5 (#10309)

* Faqcs (#10300)

* adding recipe for FaQCs software

* update test command for R

* build change to number 1

* change R to r-base

* test for no R --version

* test redirect STDERR to STDOUT

* add R testing

* provide precomplied binary for MacOSX

* build number 1 -> 0

* make OPENMP=""

* nim-falcon (#10312)

* Update nasp to v1.1.2 (#10308)

* Update nasp to v1.1.2

* lint doi and skip noarch

* build linux only

* Update meta.yaml

* add recipe-maintainers

* update bbmap to 38.20; add doi for bbmerge; misc meta.yaml cleanup. (#10310)

* Rebuild older perl-json-xs (#10313)

* Rebuild older perl-json-xs

* fix permission on mac

* Unblacklist perl-lwp-protocol-https (#10304)

* unblacklist perl-lwp-protocol-https

* bump version

* requirement

* lint

* experimental patch

* disable tests

* fix

* perl-lwp-protocol-https fix (#10317)

* Update cyvcf2 to 0.10.0 (#10314)

* Update cyvcf2 to 0.10.0

* cyvcf2: add libcurl dependency

* PacBio: Update `lima` to 1.7.1 (#10318)

* PacBio: Update `isoseq3` to 3.0.0 (#10319)

* Perl: more unblacklisting (#10305)

* more unblacklisting

* graphviz

* fix

* mac build

* mac build

* perm

* rebuild on macos

* no need to rebuild this version (see #10313)

* mac perms

* rebuild

* rebuild

* PacBio: Initial addition of `pbsv` (#10320)

* Remove r-biclust in favour of the conda-forge one. (#10322)

* Unblacklist perl-soap-lite (#10324)

* unblacklist perl-soap-lite

* rebuild mac

* mac perms

* Bt2 build (#10328)

* Changes for building bowtie 2 static binaries

* Blank out LDFLAGS

* Update seven-bridges-python to 0.15.2 (#10330)

* Update CrossMap version (0.2.7 -> 0.2.8) (#10327)

* Update python-cluster to v1.4.1.post1 (#10222)

* Update python-cluster to v1.4.1.post1

* use pip

* Update loompy to 2.0.10 (#10214)

* Update loompy to 2.0.10

* Update meta.yaml

* noarch: python

* remove loompy from build-fail-blacklist

* Update meta.yaml

* Update gridss to v1.8.1 (#10331)

* Update catch to v1.1.0 (#10225)

* Update catch to v1.1.0

* add noarch and use pip

* Build cdbtools for osx (#10329)

* Update nanopolish recipe for 0.10.1 release (#10333)

* fixed flye build error (due to zlib) - package removed from blacklist (#10335)

* fixes #10336 (#10337)

* fixes 10336

* increase build number and add test

* Update meta.yaml

* tcoffee 11.00.8cbe486 (#10130)

* tcoffee 11.00.8cbe486
* Revert meta.yaml
* Update folder name
* add DOI [ci skip]
* Fixing test
* Added t-coffee required runtime deps
* Exclude poa from MacOS build
* Add poa dependency

* Update nglview to v1.1.6 (#10339)

* lumpy: trying to fix skipped build (#10338)

* lumpy: use python version restriction instead of selector

* lumpy: pass on compiler/linker flags to make

* lumpy: add C(PLUS)?_INCLUDE_PATH exports again because the world ain't perfect

* lumpy-sv: also export LIBRARY_PATH...

* lumpy-sv: fix extractSplitReads_BwaMem path

* mac os rebuild (#10347)

* pb-dazzler-0.0.0 (#10348)

* Unblacklist bioperl (#10325)

* fix build

* add missing deps

* update bioperl version

* 3 modules which were moved out of bioperl-run in the latest version

* fix cyclic dep

* move out bio-coordinate + adapt tests everywhere

* unblacklist

* break the (vicious) cycle

* fix tests

* missing dep

* fix versions

* disable temporarily

* disable temporarily

* typos

* fix

* disable this too for now

* disable temp

* good old mac permission problem

* rebuild this one too

* another one

* bump

* bump

* bump

* another one

* bump

* bump

* bump

* bump

* Update vcftools to 0.1.16. (#10345)

* unblacklist (#10349)

* Unblacklist perl-bio-samtools (#10350)

* Unblacklist perl-bio-samtools

* mac perms

* Unblacklist perl-bio-asn1-entrezgene (#10351)

* Unblacklist perl-bioperl-run (#10352)

* increase build number

* updated scvi to v0.1.6 (#10346)

* scvi v0.1.4

* fix pytorch and python version

* fix noarch

* remove fn

* add scvi v0.1.6

* Nglview v1.1.6 (#10343)

* Update nglview to v1.1.6

* remove nglview from blacklist

* Update hyphy to 2.3.14 (#10342)

* Update hyphy to 2.3.14

* disable extended-base

* Create conda_build_config.yaml

* Update meta.yaml

* Update isatools to v0.10.3 (#10340)

* Unblacklist perl-bio-tools-* (#10353)

* Unblacklist perl-bio-tools-*

* trigger new test

* add missing dep

* we need this one on mac

* need this too on mac

* conda is confused between python and perl, it tries to import the module in perl while it's a python one

* mac perm

* t_coffee is too complicated (for me) to isntall on mac

* Update solvebio to v2.6.1 (#10220)

* Unblacklist more bioperl (#10354)

* Unblacklist more bioperl

* fixes + add extutils-makemaker

* remove obsolete checks

* Unblacklist some other perl-bio-* (#10358)

* Unblacklist some other perl-bio-*

* disable for now

* mac perm

* Update bioconda-utils to v0.14.2 (#10360)

* Update bioconda-utils to v0.14.2

* noarch: python

* Update PureCLIP recipe to v1.1.1 (#10361)

* Update beast to v1.10.1 (#10362)

* Add tandem-genotypes (#10286)

* Add tandem-genotypes

* Add tandem-genotypes license

* Add tandem-genotypes noarch

* Add tandem-genotypes host

* Update helperlibs to release-0-1-9 (#10223)

* Update helperlibs to release-0-1-9

* use pip

* Update binsanity to 0.2.6.3 (#10363)

* Update binsanity to 0.2.6.3

* add noarch

* update bioconvert to v0.2.0 (#10316)

* update bioconvert to v0.2.0

* vep: bumped major version (#10366)

* Update treetime to v0.5.0 (#10370)

* new jbrowse release (#10371)

* Unblacklist a few recipes (#10364)

* unblacklist

* lint

* bump

* typo

* force version

* fix augustus 3.2.3

* bump

* bump more

* disable repeatmasker until prl package removed from bioconda

* mac perms

* thanks @bgruening :)

* mac fix

* mac fix

* max fix

* mac fix

* typo

* typo

* trigger new test

* delay repeatmasker

* mac perms

* Fixing some perl (#10375)

* Fix perl-date-manip

* Fix perl-env-path

* Unblacklist

* Fix perl-json-parse

* Unblacklist

* Remove older perl-json-parse

* fix build number

* Rebuild perl-file-slurp (#10376)

* Update mob suite to version 1.4.8 (#10377)

* Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

* updated recipe to download from URL instead of github

* build python version requirement defined (python >=3.4)

* added build number

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added test statement (import)

* added test statement (import)

* added the new repository and py36 only compile

* made requested corrections by daler. Corrected build number and package string

* Small fixes

* revert deleted row

* New version, fixed sum bugs and improved stability

* Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters

* new version should reset the build number to 0

* nanopolish out of blacklist (#10368)

* nanopolish outof blacklist

* openmp

* cxx compiler

* config for build

* compiler mess

* skip linting for compilers to accept the hack

* Update meta.yaml

* of course old style needs libgcc

* Dpryan79 fixes 090818 1 (#10378)

* Remove various recipes from the black list

* apoc needs fortran

* skip OSX with agg

* Add bioconductor-zinbwave (#10142)

* Add r-softimpute
* Add bioconductor-zinbwave
* Fixed errors detected during linting
* Added the 'extras' section
* Removed Windows-specific lines from the r-softimpute recipe
* Forgot to remove some Windows-specific lines
* Fixed r-softimpute build.sh
* Fix source url
* Remove r-softimpute
* Add gsl dependency
* Fix gsl version
* skip macOS build

* trigger rebuild

* Remove barrnap, bfc and bgt from the black list (#10380)

* Update snippy to 4.0.0 (#10315)

* Adding a recipe for ksw (#10382)

* Adding a recipe for ksw

* lint?

* use tag as PCK_VERSION

* more

* one commit to rule them all

* cromwell uses find during runtime. With a normal conda installation it can fall back on the host installation, but when running in a biocontainer it only has access to the busybox version which lacks some necessary options. (#10383)

* Perl fix 17 (#10379)

* Fix perl-text-nsp

* Fix perl-image-exiftool

* Fix perl-test-output

* Unblacklist

* Fix shebang

* rebuild flowtools (#10385)

* flowtools

* Update meta.yaml

* skip noarch linting

* Fix typo (#10386)

* Bump perl-vcftools-vcf (#10387)

* Perl parse yapp fix (#10388)

* Bump perl-parse-yapp

* Fix typo

* Enable ensembl-vep from blacklist (#10394)

perl-bioperl now available, pin to updated version to get all
dependencies in sync. Fixes #10366

* Biobb common (#10397)

* First version of biobb_common package recipe

* Adding build noarch section and removing fn section

* Modification in no arch section

* Deleting build.sh

* Ngsplotdb bugfixes (#10396)

* Fix installation for hg19

* Fix hg38

* Fix mm10

* Better syntax

* bioconda release for Trinity v2.8.1

* bioconda updates for v2.8.1
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@arshajii