VarScan + snpEff issue #441
Comments
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Miika; The underlying issue is that the snpEff shell script greps for |
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Thanks Brad, I pulled the latest code (including the above fix) but it's still producing the error when I restart the run. Anything I could look out for? |
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Ugh apologies. It looks like having |
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@chapmanb be replaced by this: |
chapmanb
added a commit
to chapmanb/SnpEff
that referenced
this issue
Jun 24, 2014
chapmanb
added a commit
to chapmanb/homebrew-science
that referenced
this issue
Jun 24, 2014
Fixes issue with `-cancer` and `-canon` arguments passing through snpEff wrapper (bcbio/bcbio-nextgen#441). Sent upstream so can remove on next release (pcingola/SnpEff#35).
|
Miika; |
lmrodriguezr
added a commit
to lmrodriguezr/homebrew-science
that referenced
this issue
Jul 26, 2015
make arguments now handled through options, not environmental variables.
Closes #706.
update vips.rb to latest stable
also improve support for building against graphicsmagick, see:
https://github.com/jcupitt/ruby-vips/issues/50
Closes #705.
Maxima 5.32.1
Closes #701.
Vips: make core deps recommended
libvips has a lot of dependencies: some are used to implement core
functions, some are used to add support for less-used file formats.
Previously all non-required dependencies were :optional, so, by default,
libvips was missing a lot of features.
This patch tags dependencies which are used to implement vips operations
and support for common file formats as :recommended and leaves those
which are used for less-common file formats as :optional.
Closes #707.
Scalapack: add head.
Mumps: select compiler based on :mpi.
Ipopt: Upgrade to 3.11.7 and build fixes.
- Remove MPI compilers from environment as they crash the linker
- Apply patch if Mumps was built in parallel
- Add option to skip build-time tests.
Closes #656.
Catch up with upstream audit changes
ipopt: don't do work in class scope
"--universal" is propagated automatically to deps that define it
spatialite-gis: remove conflicting LDFLAG
Closes #709.
igraph 0.7.0
Update homepage to http://igraph.org.
Closes #711.
igraph: add test
gmt 4.5.12
Closes #712.
gmt 5.1.1
Add conflicts_with GMT 4, provided by gmt4 formula.
GMT build system has now moved to cmake.
Closes #473.
gmt4: move GMT 4 to new formula
Add conflicts_with current gmt.
Prior history for GMT 4 formulae preserved in gmt.rb
Batch convert http download urls from SourceForge to https
Corresponds to upstream audit changes. See Homebrew/homebrew#27041
fastx_toolkit: use resources
lp_solve: use resources
samtools: use resource
snid: use resources
openimageio: use resources
fwdpp 0.2.0 (new formula)
The 'fwdpp' template library abstracts the basic operations
required to implement forward-time simulations of population-
and quantitative-genetic models.
Closes #695.
bedops 2.4.1
Closes #713
biocgal 0.9.6-beta: New formula
The name CGAL conflicts with
Computational Geometry Algorithms Library
reapr 1.0.16: New formula
REAPR is a tool that evaluates the accuracy of a genome assembly using
mapped paired end reads, without the use of a reference genome for
comparison.
maker 2.31: Add optional dependencies for MAKER-P
infernal and trnascan
ensembl-tools 75: New formula
Tools include:
variant_effect_predictor
assembly_converter
id_history_converter
region_reporter
gmcloser 1.2: New formula
opencv 2.4.8.2
Set proper paths for python and openni. Build requires ant.
Closes #622. Closes #681.
opencv: move openni option inside block
bamutil 1.0.11
allpaths-lg: fix url
Add fails_with for GCC >=4.7 requirement.
Closes #361.
analysis 0.8.4
Closes #718.
wcstools 3.8.7 (new formula)
Closes #717.
Update R formula to 3.03
R version 3.0.3 (Warm Puppy) has been released on 2014-03-06.
See http://cran.r-project.org/src/base/NEWS.html
Closes #720.
htslib 0.2.0-rc6
samtools 0.2.0-rc6 devel
htslib: Install version.h
bcftools 0.2.0-rc6: New formula
samtools: Add option --without-bcftools
Closes #550
bcftools: Tidy up the formula
NetCDF: update to 4.3.1.1
- remove patch -- this has been merged upstream
- disable the DAP remote tests.
Closes #719.
igv 2.3.31
celera-assembler 8.1: Fails to build with clang
error: use of undeclared identifier 'use_safe_malloc_instead'
Closes #573
celera-assembler: Add a comment mentioning head
Head doesn't build, because the 'kmer' direction is missing.
tophat 2.0.11
genometools 1.5.1: New formula
Genometools is a genome analysis system that consists of a free
collection of bioinformatics tools (in the realm of genome
informatics) combined into a single binary named gt. It is based
on a C library named “libgenometools” which consists of several modules.
Closes #662
genometools 1.5.2
samtools HEAD: Fix the build
samtools: Use build.with? "dwgsim"
Use build.with? "dwgsim" instead of build.include? 'with-dwgsim'
htslib HEAD: Use git rather than a tar.gz
Use https://github.com/samtools/htslib.git
rather than https://github.com/samtools/htslib/archive/develop.tar.gz
viennarna: style cleanup
wcslib: style cleanup
Batch convert http download urls from Google Code to https
Corresponds to upstream audit changes.
R: use brewed gettext
On clean install, update.packages() was failing with:
In file included from R_systat.c:23:
./foreign.h:33:10: fatal error: 'libintl.h' file not found
Closes #676.
Add switches to x11 and Tcl/Tk
Two switches are added to allow users turn off non-crucial components, namely x11 and Tcl/Tk.
Closes #729.
openni: create and install pkg-config file
Closes #728.
R: fix args for configure
`--without-x` is missing from #133a72a and therefore configure
will not really disable x11.
Closes #730.
R: use RStudio CDN as primary download url
nco 4.4.2
Depends on newer texinfo.
Closes #725.
bedops: improve build process
Fixed optimization flags, removed unused links to libxml2 and
OpenGL libraries, other fixes
Closes #726.
MLPACK: new formula.
MLPACK is a library of machine learning algothms,
see http://mlpack.org for further information.
Closes #715.
Z3 theorem prover: new formula
Closes #289.
Z3: replace CRLF patch with inreplace
R: RStudio can find R installed via homebrew
This caveat is no longer true.
See https://support.rstudio.com/hc/en-us/articles/200486138-Using-Different-Versions-of-R
Closes #736.
vcftools 0.1.12
Closes #734.
bcftools, htslib: Add version to compile
bcftools and htslib do not correctly determine the version, reporting
0.0.1 on the command line. These correctly write out the version
information.
Closes #733.
fastx_toolkit: Fix the build on Mountain Lion
clang build fails on Mountain Lion, but works on Mavericks.
Closes #620
Armadillo: update to 4.100.2
Closes #738.
biopieces 2291: New formula
The Biopieces are a collection of bioinformatics tools that can be
pieced together in a very easy and flexible manner to perform both
simple and complex tasks.
opencv: make Java bindings optional
Prevents forcing the :ant dependency on users without Java installed
and disables Java bindings by default.
bowtie: bump fails_with :clang version
bedtools 2.19.1
Closes #742.
Suite Sparse: refactor formula.
Several make variables are defined multiple times in
SuiteSparse_config_Mac.mk and sometimes with leading blanks. This caused
change_make_var to only change some of them and led to a bug where
SuiteSparse uses Accelerate even if the user selects OpenBLAS.
This update removes change_make_var entirely. See also:
https://github.com/Homebrew/homebrew/pull/27483
opencv: make eigen dep recommended
Closes #745.
Suite Sparse: remove escaped quotes.
Mumps: refactor formula.
This update removes change_make_var entirely. See also:
https://github.com/Homebrew/homebrew/pull/27483
Xmgredit: remove change_make_var
Voro++: remove change_make_var.
Velvet: remove change_make_var
Trnascan: remove change_make_var
Scotch5: remove change_make_var
Scotch: remove change_make_var
igvtools 2.3.31 (new formula)
Closes #746.
maxima: Fix test command by removing `'`
maxima was receiving the command `'run_testsuite(); quit();'`,
which just delayed the execution of the function
Closes #747.
gaemr 1.0.1: New formula
Genome Assembly Evaluation Metrics and Reporting (GAEMR):
a comprehensive package for assembly analysis
gmap-gsnap 2014-02-28
bowtie2 2.2.1
Remove upstreamed patch.
Closes #748.
Scotch5: build shared libs.
Scalapack: option to build shared libs.
piler 1.0: New formula
PILER is public domain software for analyzing repetitive DNA found in
genome sequences.
repeatscout 1.0.5: New formula
RepeatScout is a tool to discover repetitive substrings in DNA.
recon 1.05: New formula
The RECON package performs de novo identification and classification
of repeat sequence families from genomic sequences.
recon 1.07
The 1.07 version fixes problems with running RECON on 64 bit machines
and supplies a workaround to a division by zero bug.
Tmv-Cpp: New formula.
Closes #544.
Petsc: upgrade to 3.4.4.
quicktree: new download url
Closes #754.
giira 20140221: New formula
GIIRA is a stand-alone java program to predict genes based on RNA-Seq
reads without requiring any a-priori knowledge.
root 5.34.18
Closes #750.
allpaths-lg: fails_with any clang version
Bump fails_with clang versions
kraken 0.10.3-beta
snpeff 3.5e
snpeff: set share dir for downloads
Move snpEff.config to #{share} and keeps jars in #{libexec}, downloads
are extracted into #{share}/data.
giira: fix audit warnings
viennarna: fix audit warnings
mrbayes: fix audit warnings
openimageio: fix audit warnings
h5utils: use checksummed patches
tmv-cpp: use checksummed patches
Metis4: build shared lib and add tests.
Metis: build shared lib.
ASL: upgrade to latest version.
samtools: Patch dwgsim mut.c error
Fixes #759.
Fix mlpack dependency on C++11 library versions
Closes #761.
aragorn 1.2.36: New formula
tRNA and tmRNA detection
tbl2asn 23.0: New formula
Tbl2asn is a command-line program that automates the creation of
sequence records for submission to GenBank.
prokka 1.8: New formula
Prokka is a software tool for the rapid annotation of prokaryotic
genomes.
rmblast 2.2.28: New formula
RMBlast is a RepeatMasker compatible version of the standard NCBI
BLAST suite. The primary difference between this distribution and the
NCBI distribution is the addition of a new program "rmblastn" for use
with RepeatMasker and RepeatModeler.
Fix `brew audit` warnings.
suite-sparse: add mirror url
Closes #762.
gdcm 2.4.1 (new formula)
Closes #751.
flann: fix `--with-examples` patch condition
ucsc-genome-browser 296
repeatmasker: Use RMBlast by default
repeatmodeler 1.0.7: New formula
RepeatModeler is a de-novo repeat family identification and modeling
package.
cddlib: add mirror
pspp: add mirror
root: use checksummed patch
Add fossies.org mirror.
sickle: use checksummed patch
astrometry-net 0.46 (new formula)
A package for automated calibration of astronomical images.
Closes #385.
muscle: replace patch containing CRLF
arpack: improved BLAS support (both openBLAS and vecLib)
Closes #768.
nlopt: fix audit warnings
fastq-tools 0.6 (new formula)
Add formula for Daniel Jones's FASTQ processing toolkit, fastq-tools
Closes #769.
blast 2.2.29
Release Notes: http://www.ncbi.nlm.nih.gov/books/NBK131777/
arpack.rb: comment correction.
Closes #778.
genewise: Fix build error on Linux
Replace isnumber with isdigit to fix the error:
undefined reference to `isnumber'
Tested with GCC 4.4.7
Closes #775
wcslib 4.21
Closes #780.
genewise: Apply the patch regardless of OS
hdf5: remove duplicate option
Add warnings for enable-threadsafe conflicts.
insighttoolkit: build hdf5 with :cxx11
Bump TMV-CPP version to 0.72
Closes #782.
add gal-sim: a galaxy simulation toolbox.
GalSim is a package for simulating astronomical images of galaxies.
It was developed to support the upcoming "Great3" challenge,
http://great3challenge.info/, to test different methods for measuring
weak gravitational lensing, a key way of measuring mass in the
universe through its bending of light.
Closes #545.
Vigra: add cxx11 option, fix python site-packages install path
Closes #774.
Vcftools: updated to version 0.1.12a
Closes #784.
suite-sparse: Fix conflicting openblas dependencies
Fixes breakage with numpy --with-openblas because of conflicting
dependencies: numpy asks for homebrew/science/openblas while suite-sparse
just asked for openblas, and homebrew did not realize they were the same
thing. This seems to be a recurring issue that was causing a lot of problems.
Closes #767. Fixes Homebrew/homebrew#27752.
vcftools: force new version
Override alpha/beta versioning for new release.
hotspot 4.0.0 (new formula)
Closes #739.
hotspot: add test to caveats
Migrate dotwrp, qrupdate, slicot to homebrew-science
picard-tools: update to version 1.110
Closes #788.
Import hwloc from core
Remove reference to homebrew/science tap in dependencies.
Closes #767.
snpeff 3.5g
Closes #792.
pocl: migrate from core.
SExtractor: new formula.
Closes #753.
Hdf5: Add option for C++ bindings
Closes #795.
t-coffee 10.00.r1613: New formula
A collection of tools for Computing, Evaluating and Manipulating
Multiple Alignments of DNA, RNA, Protein Sequences and Structures
vcftools: use debian-style versioning.
x.xxa is incorrectly recognized as an alpha release, and x.xxa_1 is
perpetually seen as outdated.
phlawd 3.4a: New formula
Mega-phylogeny approach for comparative biology: an alternative to
supertree and supermatrix approaches
Closes #789
spades: Add DOI
idba 1.1.1: New formula
IDBA is a practical iterative De Bruijn Graph De Novo Assembler for
sequence assembly in bioinfomatics.
idba: Do not install bin/test
Install generically named programs in libexec.
Lammps: update PYTHONPATH info in caveats.
Closes #797.
MB-System: New formula.
Pastix: bug fix release.
last 418: New formula
LAST finds similar regions between sequences.
openblas: Remove outdated comment
I made that comment ages ago when OpenBLAS did download an LAPACK
on-demand during build. This is no longer the case as far as I can tell.
openblas: 0.2.9rc2
Going to a RC here (exceptionally) because on newer Macs (I tested on
two, one haswell and one Mac Pro) the CPU auto detection fails and
formula install aborts. Also if we would force a certain TARGET, the
logic for that would be quite complicated. Further, the test did not
pass on a haswell based system. I hope this does not break other
software Homebrew/science.
openblas: Need to add version number explicitly
maker: Add DOI
opencv: add options --with-tests, --without-openexr
Force brewed libs for all dependencies. Style cleanup.
samtools: update dwgsim to 0.1.11
Closes #801.
allpaths-lg: fix url
MTL: upgrade to 4.0.9507.
Closes #804.
SLEPc: upgrade to 3.4.4.
picard-tools 1.111
Closes #807
picard-tools: Add a test
giira: fix url
Newer release removed by upstream.
quast 2.3
Add a DOI.
prodigal: update url, add HEAD
Development moved to GitHub.
oce 0.15
Closes #803.
edirect 1.60
glimmerhmm 3.0.2: New formula
GlimmerHMM
Eukaryotic Gene-Finding System
igv 2.3.32
cufflinks 2.2.0
Builds with latest clang, linked against bottled Boost.
ucsc-genome-browser 297
atpdec 1.7 (new formula)
NOAA POES weather satellite image software decoder.
Closes #799.
snp_sites 1.5.0
bwa 0.7.8
ensembl-tools: fix url
ensembl-tools: update sha1
Catch up with latest changes to release/75 branch.
Add caveat to ammend PERL5LIB with libexec.
lumpy-sv 0.2.0
Also removes GSL dependency and patch, simplifying build.
Closes #812.
radx 20140401
Add contributing guidelines to root.
New formula: Lis 1.4.34
Closes #806.
augustus: Fails to build with clang 503
Closes #818
radx: hdf5 must be built with cxx
Closes #816.
delly 0.3.3
Add option to install 64-bit binary on Linux.
Closes #813.
R 3.1.0
R 3.1.0 (codename "Spring Dance") was released April 10, 2014.
More information at:
https://stat.ethz.ch/pipermail/r-announce/2014/000572.html
Closes #815.
Closes #821.
bedops 2.4.2
Closes #820.
bowtie 1.0.1
graph-tool 2.2.31
Closes #802.
insighttoolkit 4.5.2
Closes #824.
bowtie2 2.2.2
hotspot 4.1.0
Closes #827
ucsc-genome-browser 298
scarpa 0.241: New formula
Scarpa is a stand-alone scaffolding tool for NGS data. It can be used
together with virtually any genome assembler and any NGS read mapper
that supports SAM format.
snpeff 3.5h
igvtools 2.3.32
R: link with Accelerate framework
By default R should link against the Accelerate framework.
Closes #825.
field3d 1.4.3
lammps: install examples dir
Closes #808.
orocos-kdl 1.2.2 (new formula)
Closes #415.
sais 2.4.1: New formula
An implementation of the induced sorting algorithm
sais is a very simple and small library that provides an
implementation of the induced sorting [1] based suffix array
construction algorithm. The algorithm runs in O(n) worst-case time,
and MAX(2n, 4k) worst-case extra working space, where n and k are the
length of the input string and the number of alphabets.
Fix audit warnings
openbr 0.4.1 (new formula)
OpenBR is an open source framework, supplying face recognition and
related functionality. OpenBR is a a communal biometrics framework
supporting the development of open algorithms and reproducible evaluations.
OpenBR is supported on Windows, Mac OS X, and Debian Linux. The project is
licensed under Apache 2.0 and releases follow the Semantic Versioning
convention. Internally the code base uses the CMake build system and
requires Qt and OpenCV.
Closes #494.
opencv: Add --with-cuda, require -stdlib=libstdc++ when enabled
Closes #305.
picard-tools 1.112
Closes #840.
r-gui 1.64 (new formula)
New formula for the R Mac GUI.
The following restrictions hold (based on the `INSTALL` instructions):
> Only Mac OS X 10.6 and higher are supported, and only 64-bit R
R.app is linked against the installed version of R (in opt).
HEAD version works via SVN repo (employs a minor hack due to the build
scripts requiring the SVN version).
Closes #831.
barrnap 0.3: New formula
Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes
in Bacterial and Archaeal genome sequences. It takes FASTA DNA
sequence as input, and write GFF3 as output.
prokka: Depends on barrnap
prodigal: Add DOI
prokka: Add DOI
snap: Fix the ZOE path
Add DOI
maker: Symlink gff3_merge
repeatmasker: Add instructions to caveats
repeatmodeler: Symlink BuildDatabase
prokka: Install the large database
Closes #800
sailfish: Add DOI
R: add path to OpenBLAS lib, without-accelerate option
OpenCV: support for --head install.
Closes #848.
Update to version 8.0.20
Closes #847.
Fix x11 dependency.
See Homebrew/homebrew#28096.
Fix x11 dependency guideline.
See Homebrew/homebrew#28096.
Closes #846.
libccd: collision detection between convex shapes
This is used by the dartsim and gazebo robotic simulators for
collision checking.
Closes #811.
consed 27.0: New formula
A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish,
Autoreport, Autoedit, and Align Reads To Reference Sequence)
edirect 1.70
CONTRIBUTING: add Table of Contents, adjust heading style
viennarna 2.1.7
reapr 1.0.17
Fixes #851.
igv: Add DOI and head
bali-phy 2.3.0
Closes #852.
bedops: update sha1
mbsystem 5.4.2183
abyss 1.5.0
Add DOI
trans-abyss: Add DOI
bali-phy 2.3.1
Closes #855.
maker 2.31.3
root: revert to X11 for default backend
Closes #854.
Reverts f1ecc89.
radx 20140417
therion 5.3.14 (new formula)
Closes #758.
blast: set dependency options
Dependencies are explicitly turned off or paths set to opt_prefix.
Closes #542.
SuperLU: new formula.
Thanks to @ysakamoto86
Closes #721.
snoscan 0.9b: New formula
Search for C/D box methylation guide snoRNA genes in a genomic
sequence
maker: Add an optional dependency on snoscan
viennarna: Requires X11 for RNAforester
mir-prefer 0.16: New formula
miR-PREFeR: microRNA PREdiction From small RNAseq data
maker: Add an optional dependency on mir-prefer
viennarna: ENV.deparallelize for make install
ASL: changes to use with linuxbrew.
Closes #857.
genometools: depends on pkg-config
wcslib 4.22
Closes #859.
samtools: Add DOI
opencv 2.4.9
Closes #865.
Closes #862.
lumpy-sv 0.2.1
Closes #864.
maker 2.31.4
abyss 1.5.1
maker: Add the DOI of MAKER2
maker: Add license info to caveats
ucsc-genome-browser 299
picard-tools 1.113
Closes #870.
edirect: update sha1sum
alembic 1.5.4
Closes #403.
oce: remove X11 dependency
OCE does not use X11 on Mac OS X.
Closes #856.
opencv: switch eigen and openexr to optional
Eigen and OpenEXR are special-case (interoperability) libraries and
are not needed for general purpose usage of OpenCV.
Closes #874.
igraph 0.7.1
Closes #878.
gmt: add full mirror list.
Adding all available mirrors to gmt formula, since
people are experiencing download problems from the main
site.
Closes #876.
openni: fix typo in pkg-config file path
Closes #882.
openni: use checksummed patches
tabix: conflicts with htslib
barrnap 0.4
opencv: make jasper dependency optional
Closes #875.
prokka 1.9
barrnap 0.4.2
bamtools: use checksummed patch
root: Fix compilation error with X11 backend
ROOT compilation with X11 backend may fail if there is a clash between
homebrewed freetype>=2.5.1 in /usr/local/include/freetype and XQuartz
freetype<2.5.1. This patch rises XQuartz'es includes priority so that
clang doesn't try to halfbreed freetype headers.
Closes #853.
Closes #868.
hmmer: Add DOI
hmmer2 2.3.2: New formula
sga: Add DOI
smrtanalysis 2.2.0.133377: New formula
blasr 2.1: Fails to build with clang and gcc-4.2
exonerate 2.2.0: Add DOI and a test
maker: Make most dependencies optional
Add DOI
openni: fix patch shasums
Closes #888.
htslib 0.2.0-rc8
Closes #881.
bcftools 0.2.0-rc8
Closes #880.
mcl 14-136
Closes #890.
mcl 14-137
Closes #895.
netcdf 4.3.2
Closes #892.
hdf5 1.8.13
Closes #893.
octave 3.8.1: optional GUI & JIT
Squashed these commits:
Support suite-sparse built with metis4
Removed X11 dependancy
Removed X11 dependancy, we don’t need it for Mac at all, because we
build with native Qt. (+9 squashed commits)
Squashed commits:
[c0d9779] Fixes X11 Problem
Remove hack with X11 lib, because homebrew removes it anyway.
https://github.com/Homebrew/homebrew-science/pull/723#issuecomment-42023
408
Added regular x11 depends_on
[f32ba8e] Moved the X11 replacement to the proper place
[85d53b3] Added X11 lib path fix back in
[2364e7e] Further remove unnecessary link dependencies in mkoctfile.
[f5ec7bd] Removed the keyboard patch for HEAD builds; added mkoctfile patch, pstoedit/epstool dependencies
[3050c2a] EXPERIMENT: stripping out extra link dependencies in mkoctfile, to see if it fixes the pkg problems.
[ac7b8eb] X11/TeX fixes
[c72b81f] Fix for odd mkoctfile dependency issues
[a671276] octave 3.8.1: optional GUI & JIT
Closes #723.
moab 4.6.2
Also use --libdir=libexec/lib
Closes #891.
Mathgl 2.2.2.1
Add tetgen
alembic: update url, add HEAD
alembic: use hg release tag
Google Code seems to generate differing tag archives each download.
Fix audit warnings
cmor 2.9.1 (new formula)
CMOR is Climate Model Output Rewriter, which is a standard tool for
transforming climate model output data into standard form. For more
information, see http://www2-pcmdi.llnl.gov/cmor.
Closes #860.
tetgen 1.5.0
TetGen is a program to generate tetrahedral meshes of any 3D
polyhedral domains.
Closes #899.
gmsh 2.8.4
Gmsh is a 3D finite element grid generator with a build-in CAD engine
and post-processor.
Closes #872.
lumpy-sv 0.2.2.2
Closes #898.
wcslib 4.23
Closes #903.
root: cocoa as default, :x11 optional
* fix building without XCode
* disable old workaround
* refactor argument list
Closes #889.
lammps: fix path to gfortran
gfortran formula was removed in favor of gcc.
Full path to libgfortran currently:
/usr/local/opt/gcc/lib/gcc/x86_64-apple-darwin13.2.0/4.8.2/
Fixes #904.
bwa 0.7.9a
gmap-gsnap 2014-05-15
Add DOI
maker 2.31.5
pbsuite 14.5.13: New formula
Software for Long-Read Sequencing Data from PacBio
PBJelly - the genome upgrading tool
PBHoney - the structural variation discovery tool
root: tab -> spaces
genometools: Add head and DOI
bedtools: Add DOI
samtools: add vcfutils.pl to without-bcftools
vcfutils.pl is now included in the latest bcftools release candidate
(rc8) so conflicts when installed alongside samtools. This removes the
conflict when passing --without-bcftools. chapmanb/bcbio-nextgen#426
Closes #910.
root: patch not required with HEAD
Patch is only required for non-HEAD users at or before 5.34.18
without XCode installed.
Closes #905.
spatialite-gis: fix compilation with wxWidgets 3
See also https://github.com/Homebrew/homebrew/commit/b31227d6ef602142ea399b04211d306eaaea674c
Closes #298.
Closes #456.
galib: fix clang error with undeclared identifiers
Closes #908.
mummer: Add DOI
netcdf: patch to fix hdf5 1.8.13 missing symbols
HDF5 1.8.13 removes symbols related to MPI POSIX VFD, leading to
errors when linking hdf5 and netcdf5 such as "undefined reference to
`_H5Pset_fapl_mpiposix’".
The patch has already been added to netcdf, and will be included
in the next release.
Fixes #911.
Closes #916.
armadillo 4.300.3
Copy examples/ directory to prefix.
Closes #912.
bali-phy: switch to needs :cxx11
Closes #925.
bali-phy 2.3.4
Closes #922.
root: tabs -> spaces
ensembl-tools: update shasum, add head
therion 5.3.15
Closes #924.
htslib: Remove razf
razf has been removed in HEAD. See
https://github.com/samtools/htslib/pull/74
htslib: Conflicts with tabix
Both htslib and tabix install bin/tabix
htslib: Add a test
samtools: Do not build razip
razip has been removed upstream. See
https://github.com/samtools/htslib/pull/74
samtools: Fix a typo. Htslib should be htslib
samtools: 0.2.0-rc8 devel
elph: fails with clang
ucsc-genome-browser 300
ceres-solver 1.9.0, update home page
Closes #928.
mathgl: support Qt 4 or 5 with option parameter
Fixes #897.
Closes #923.
kmergenie 1.6476
Add DOI
cube 4.2.2: New formula
Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional
performance space consisting of the dimensions (i) performance metric,
(ii) call path, and (iii) system resource.
snpeff 3.6c
Closes #935.
paml 4.8
graph-tool: fix dep; flag changes; add test
Build failure fixed by requiring Python on Boost dependency.
Sparsehash dependency is recommended offically. Since the sparsehash
installation problem on 10.9.2 is now fixed (Homebrew/homebrew#27652),
it should be enabled by default.
Add option to drop Cairo dependency.
Add test based on the official quick start example
(http://graph-tool.skewed.de/static/doc/quickstart.html).
Closes #917.
nlopt 2.4.2
Closes #937.
cminpack 1.3.4
Closes #936.
bowtie2 2.2.3
cppad 20140000.3
hmmer: add make check
bowtie2: use test from examples
libpll 1.0.0 (new formula)
PLL is a highly optimized, parallized software library to ease the
development of new software tools dealing with phylogenetic inference.
(http://www.libpll.org)
Closes #901.
openimageio 1.4.8
Closes #921.
data-science-toolbox 077c94f
bowtie: add test suite, fails with gcc-4.8
Refactor for tests, switch to more complete package archive.
Closes #885.
pykep 1.1.3 (new formula)
Closes #194.
spades 3.1.0
lightstringgraph 0.1.0: New formula
Lightweight String Graph Construction
spades: use --test for test
Closes #934.
README: update links
cube: Add qt to recommended dependencies
Fix make arguments.
Closes #941.
Remove unicode quotes
vcftools: add option for brewed zlib
Fixes #944.
cdsclient: force correct mandir
gmsh: Build also as library
Closes #950.
gmsh: remove trailing whitespace
bioawk: tag stable release
libpll: fix audit warning
stacks: fails with clang
Fixes #955.
cantera: migrate from Homebrew core
Closes #948.
Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
gromacs: migrate from Homebrew core
Closes #947.
Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
sundials: migrate from Homebrew core
Closes #946.
Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
gromacs 4.6.5
Perform build-time tests.
Closes #959.
nfft 3.2.3: new Formula
Closes #396.
plink: Patch to fix build, add test
Closes #958.
hypre 2.9.0b
Hypre is a library of high performance preconditioners that features
parallel multigrid methods for both structured and unstructured grid
problems.
Closes #906.
megam 0.9.2: Maximum entropy machine learning package
megam and megam.opt (the optimized version) are machine learning commandline tools
used by Python NLP Toolkit (nltk) if the built in libraries are too slow.
Closes #949.
Use File.exist? instead of File.exists?
File.exists? is deprecated in Ruby 2.1+.
ASL: option to build Matlab interface.
Bump gal-sim to release 1.1.0
Closes #960.
cube: Fails to build with clang
Undefined symbols for architecture x86_64:
"cube::Cube::def_mirror(std::string const&)", referenced from:
MainWidget::readFile(QString) in cube-MainWidget.o
R: Fix head build.
Closes #405.
blasr: Specify the path to hdf5
Closes #932
sundials: add features
- add serial tests for C bindings
- add patches from mailing list since 2.5.0 release
- add openblas support
- add Fortran support
- add serial Fortran tests
- add mpi support
- add parallel tests for C bindings
- add parallel tests for Fortran bindings
- add patches (submitted upstream) to fix additioanl bugs
- add Argonne PETSc project mirror
Closes #962.
Healpix version 3.11
See http://healpix.jpl.nasa.gov/
HEALPix is an acronym for Hierarchical Equal Area isoLatitude
Pixelization of a sphere. As suggested in the name, this pixelization
produces a subdivision of a spherical surface in which each pixel
covers the same surface area as every other pixel. Healpix is used
extensively in astronomy to produce maps of data on the sky.
Closes #169.
qcl: 0.6.4: a language for quantum computers
Wikipedia lists QCL as one of the first quantum programming languages. This formula downloads and installs the latest version of QCL from the maintainer's website. In addition, the formula copies the standard QCL library so that the interpreter is able to run properly.
Closes #288.
mafft: fix build error on 10.6
Closes #313.
ropebwt2 r181
Add a link to the PDF on arXiv.
Sara: 1.13 - Deciding reachability for Petri nets
Sara is a tool for solving the reachability problem for Petri nets. Given a
low-level Petri net, i.e. sets of places and transitions with weighted arcs
between them, and an initial and a final marking, Sara tries to determine
whether the final marking can be reached from the initial marking by firing a
sequence of transitions in the Petri net. While the initial marking must be a
map from the places to non-negative integers, that means one single marking,
the final marking can be somewhat generalized. It is possible -- for each place
on its own -- to declare that the given number must be reached exactly (as for
the initial marking), covered (a higher value is allowed), or bounded (a lower
value is permissible). In addition, more general constraints may be formulated
which the final marking must fulfill. Such a constraint can be any linear
(in)equation built from places and transitions.
As a by-product, also problems of form ``given a Petri net, an initial marking,
and a transition multiset, is the multiset realizable?'' can be solved.
Realizable means that there is a firing sequence in the Petri net that contains
each transition exactly as often as the transition multiset dictates.
If Sara can compute the problem given, it should either tell the user that
there is a solution and present a firing sequence proving this, or it should
tell that the problem is infeasible. In the latter case, Sara might provide
additional information that gives some insight into why the problem is
infeasible.
Closes #349.
PNAPI: 4.03 - A C++ Petri Net API
The Petri Net API is a C++ library of Petri net-related functions. It is
currently used in more than a dozen Petri net tools, ranging from compilers
to verification tools.
Closes #353.
Migrate vtk5 back from homebrew-versions
vtk: use patch DSL
Mira: upgrade to 4.0.2.
The Boost libraries aren't discovered unless they are passed to make.
Closes #968.
Upgrade asl to v20140617.
Closes #978.
version 6.7.1
Closes #972.
delly 0.5.5
Closes #974.
sratoolkit: version 2.3.5-2
Closes #965.
Ipopt: upgrade to 3.11.8
Scotch: build shared libs and run tests.
Include a patch to fix the ptcheck tests and to correct an omission
in the tests Makefile.
asl 20140618
Closes #981.
New formula: getdp 2.4.3
Closes #945.
vecLibFort 0.2: new formula
Closes #765.
Velvet: fix options for command-line arguments.
Closes #985.
Velvet: fix default CATEGORIES value.
Closes #986.
tisean: new formula
Closes #980.
picard-tools: upgrade to 1.115
Closes #982.
Colpack: option to build against libc++
Adol-C: upgrade to 2.5.0.
Closes #793.
Install LUSOL headers in lp_solve
Closes #657.
Getdp: Fix Gmsh lib destination.
vecLibFort: upgrade to 0.3.0.
Arpack: use double quotes.
Arpack/QRUpdate/Scalapack: use vecLibFort.
Many thanks to @mcg1969!
Fixes #7. Fixes #293.
Enblend-enfuse: fix option.
Update MBSystem version to 5.4.2191
Closes #987.
clustal-w: Fails to build with clang
Closes #967
clustal-w: Add a test
clustal-w: Add a DOI
masurca: Requires pkg-config
masurca: Fails to build on Mac OS
masurca: Add DOI
masurca 2.2.1
fcgene: new formula
Closes #956.
mira: fix audit warning
orocos-kdl: use spec dependencies
pnapi: use spec dependencies
r: use spec dependencies
sara: use spec dependencies
htslib 0.2.0-rc9
Closes #998.
bcftools 0.2.0-rc9
Closes #999.
pspp: 0.8.3: fix GUI issues
Closes #1001.
mafft 7.157 + new test
Closes #1005.
R: add test.
Closes #1007.
Tisean: Add caveats.
Closes #993.
gdcm: 2.4.2
Closes #1002.
snpeff: fix bug in wrapper script
Fixes issue with `-cancer` and `-canon` arguments passing through snpEff wrapper (chapmanb/bcbio-nextgen#441). Sent upstream so can remove on next release (pcingola/SnpEff#35).
Closes #1006.
Maxima 5.33.0
Closes #1011.
CCfits 2.4 w/ Mavericks patch
Closes #1014.
Elemental 0.84-p1
Elemental is an open-source library for distributed-memory dense
linear algebra which attempts to strike a careful balance between ease
of use and high performance.
Closes #988.
Honor user-specified compiler.
wxMaxima 13.04.2
Closes #1022.
hwloc 1.9
Closes #1018.
veclibfort: use all lowercase.
Closes #1023.
Suite-Sparse: add correct path to libmetis v4.
Ceres-solver: pass explicit path to libmetis v4.
LoLA: Updated to LoLA 2.0
Closes #990.
Symphony: upgrade to 5.5.7.
Closes #873.
JoinX: exit with error message on OSX.
Closes #939.
Revert "htslib: Install version.h"
This reverts commit 71634ba8bebd92719c287f3d5a1d6e085a8a1e76.
Closes #1015
libsequence 1.8.2
Update to latest version of libsequence to fix compile issues on
Mavericks with clang (among other issues). Also changes download
location to github repository releases.
Closes #1029.
healpix: depends on pkg-config
Closes #1013.
swetest 2.00.00
Closes #927.
masurca: Fix No rule to make target `src/masurca'
Closes #94
Tophat: upgrade to 2.0.12.
Closes #963.
htslib 0.2.0-rc10
bcftools: Remove dependency on htslib/version.h
See #1015
bcftools 0.2.0-rc10
ucsc-genome-browser 301
bedtools 2.20.1
Symphony: Add readline support.
ensembl-tools: update shasum
fcgene: update shasum
mira: Remove dependency on homebrew/dupes/zlib
Closes #1037
Vips: update to 7.40.3
update vips.rb to latest stable, list of changes here:
http://libvips.blogspot.co.uk/2014/06/new-stable-version-740.html
add the new libgsf-1 optional dep
reorder the formula to get all recommended and all optional deps listed
together
Closes #1035.
igv 2.3.34
Closes #1048.
nextflow 0.8.3: New formula
Closes #1039
gmsh: update to 2.8.5
Closes #1052.
ASL: upgrade to 20140704
Fixes #1056.
kmerstream 1.0: New formula
KmerStream: Streaming algorithms for k-mer abundance estimation
bowtie: fix build with gcc-4.8
ucsc-genome-browser 302
openblas 0.2.9
Add --devel 0.2.10-rc2.
Closes #1038.
tbl2asn 23.6
Use patch DSL
emboss: add mirror
gmt4: update gshhg resource
gmt: update gshhg resource
getdp: update to 2.4.4
Removed the library fix (line 55) because now also corrected upstream
Closes #1061.
R 3.1.1
Release notes: https://stat.ethz.ch/pipermail/r-announce/2014/000575.html
Closes #1058.
arpack: fix symlink overwriting pkgconfig directory
Closes #1059.
bwa 0.7.10
genometools 1.5.3
openbr: fix version
jellyfish 2.1.3
Builds with newer compilers.
edirect 1.80
cap3: fix linux shasum
gdcm: use mirror selector
cufflinks 2.2.1
openblas 0.2.10
galfit 3.0.5 (new formula)
Closes #1017.
kissplice 2.2.0
update vips to latest stable, 7.40.4
this set of minor fixes help the ruby-vips gem pass all spec tests, see:
https://github.com/jcupitt/libvips/blob/master/ChangeLog
Closes #1064.
Adol-C: upgrade to 2.5.1.
augustus: add mirror
rml-mmc 274
kissplice: Use --disable-epsv
Use --disable-epsv rather than --no-epsv. The latter does not work with older
versions of curl.
fastqc: update to 0.11.2
Closes #1072.
R: option to build libRmath only.
Closes #1067.
Abyss 1.5.2
Closes #1065.
ASL: update to 20140718.
R: add explicit paths to readline.
blast: Fails to build with gcc 4.9
error: must #include <typeinfo> before using typeid
Closes #1078
vecfortlib: 0.4.0 - Updated new version
Updated to version 0.4.0, points to new cblas.h location on Mavericks
Fixes issue with sgemv_ when data is not aligned to 8-byte boundaries
Closes #1083.
emboss: skip build time embossupdate
Missing update mirror causing build failure.
pymol: fix patch args and shasum
Fixes #1082.
sextractor: revert "Use patch DSL"
bowtie 1.1.0
trans-abyss 1.5.1
bowtie: avoid staging source files
bowtie: fix bowtie bin symlink
htslib 0.2.0-rc11
samtools: 0.2.0-rc11 devel
atram 1.03: New formula
aTRAM: automated Target Restricted Assembly Method
Closes #1079
ncview: add mirror
Closes #1084.
bwa: Fix test
The test failed on Linux because the test FASTA file was incorrectly formatted.
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes
at bntseq.c line 270
bcftools 0.2.0-rc11
Fixes build issue with already upgraded htslib (chapmanb/bcbio-nextgen#519).
Removes no longer needed htslib version replacement.
Closes #1085.
APL: new formula.
ASL: update to 20140723.
Closes #1088.
JBLAS: new formula.
cantera: new formula for Cantera 2.1
Closes #1090.
Cuba: new formula
Closes #1089.
Veclibfort: fails for OSX <= 10.6
The failure is due to missing LAPACK symbols in the vecLib framework.
Fixes #1074.
new formula: openni2 2.2.0.33
Closes #1076.
trans-abyss: python-igraph requires igraph
daligner 2014-07-10: New formula
Find all significant local alignments between reads
barrnap 0.5
prokka 1.10
Netcdf: Add mirrors for two resources.
Closes #1092.
lumpy-sv: v0.2.4 and de-parallelize
Update to latest lumpy version (with Perl scripts for speedseq
compatibility) and de-parallelize make file to try and avoid issues
building on CentOS5 with gcc-4.1
Closes #1096.
minc: bump fails_with clang
Fixes #1095.
fasta: Add DOI
kissplice 2.2.1
root: upgrade to 5.34.19, workaround ROOT-5773
https://sft.its.cern.ch/jira/browse/ROOT-5773
Fixes #1094.
Closes #1098.
picard-tools 1.118
Closes #1099.
Remove duplicate.
Veclibfort: upgrade to 0.4.1.
Resolves issues with inexistent symbols on Snow Leopard.
uniqtag 1.0: New formula
Abbreviate strings to short unique identifiers.
UniqTag: Assign unique, reasonably stable, content-derived identifiers to genes
Shaun D. Jackman, Joerg Bohlmann, Inanc Birol
mumps: don't access Tab internals
tisean: use the tab for reflection in the test
radx: fix url, audit warnings
blat: style cleanup
z3: style cleanup
mir-prefer 0.19
Closes #1102.
Use new-style test definitions
r: use stable prefix for gettext and readline
Closes #1103.
hdf5: modernize, group enable-cxx and cxx11
Clean up tab usage
Inside `test` blocks, `build` is now redefined to return
`Tab.for_formula(self)`. It supports the same interface as the normal
`build`: with?, without?, include?, universal?, cxx11?, and
build_32_bit?.
Openni: update patch sha1.
insighttoolkit 4.6.0
Added SCIFIO module
Closes #1100.
new formula: MADlib 1.6.0.
MADlib: Big Data Machine Learning in SQL for Data Scientists.
MADlib is a library that allows you to apply many statistical
and machine learning algorithms to data that resides in a DBMS
(PostgreSQL).
Closes #1057.
OpenNI2: Fix patch shasum
Closes #1108.
Xylib: new formula.
Closes #918.
stacks 1.20
Add DOI.
cdo: cleanup, use opt_prefix
gmt: cleanup, use opt_prefix
ensembl-tools: reorder PERL5LIB
astrometry-net: use opt prefixes
ucsc-genome-browser 303
gdcm: 2.4.3
Closes #1113.
graph-tool: add support for --with-python3
Closes #1073.
wxmaxima: add support for --HEAD
Closes #1116.
vcftools 0.1.12b
Closes #1114.
SuiteSparse: install Matlab interfaces.
delly 0.5.6
Closes #1118.
oce 0.16
Update to 0.16
Add options for new opencl support
Closes #1115.
gmt4: add mirror, opt_prefix
edirect 1.90
sextractor: use patch DSL
emboss: add mirror, option to run embossupdate
CONTRIBUTING: move Issues on top, condense
Use stable opt_lib path
graph-tool: avoid hard-coding /usr/local
Use stable opt paths
opencv: broaden python support
Python lib and Headers directory missing from Anaconda.
Closes #843.
CONTRIBUTING: fix notes link, cleanup
opencv: support Python versions
nextflow 0.8.5
Add new :java dependency.
Closes #1068.
vislcg3: 0.9.8.10063 (new formula)
Closes #1120.
vislcg3: access Formula for path
Avoid hard-coding /usr/local prefix.
r: Fix the build for Linuxbrew
mira: google-perftools is recommended
mira: Fix test
beast: Fix naming of directory in HEAD install.
Closes #1123.
vips 7.40.5
7.40.5 has some very useful improvements to vipsthumbnail and to
openslide support
Closes #1122.
platanus 1.2.1: New formula
Genome assembler for highly heterozygous samples and large genomes.
nextflow 0.9.0
Mumps: fix doc+examples install location.
jellyfish-1.1 1.1.11: New formula
Kat depends on jellyfish 1.1.
kat 1.0.5: New formula
KAT is a suite of tools that analyse jellyfish kmer hashes.
quake 0.3: New formula
Quake is a package to correct substitution sequencing errors in experiments
with deep coverage (e.g. >15X), specifically intended for Illumina sequencing
reads.
musket 1.1: New formula
Musket is an efficient multistage k-mer based corrector for Illumina short read
data.
rampart 0.9.0: New formula
Rampart is both a pipeline for creating multiple assemblies and a framework for
analysing and comparing them.
sickle 1.33
Closes #1125
rampart: sspace has no formula
allpaths-lg: Add DOI
allpaths-lg 50378
rampart: Change the head branch to develop
New Recipe: BLAS and LAPACK manpages
Closes #1128.
bowtie2: Add DOI
aragorn: Add DOI
infernal: Add DOI
infernal 1.1.1
uniqtag: Add DOI
htslib 1.0
bcftools 1.0
samtools devel 1.0
Keep 0.1.19 as stable and 1.0 as devel, for now.
Mumps: fix location of tests.
vtk5: apply upstream patches
Closes #1135.
atram 1.04
Updating aTRAM version to one that puts config.txt into the main aTRAM
directory.
Closes #1137.
Adol-C: upgrade to 2.5.2.
Ipopt: upgrade to 3.11.9.
lumpy-sv: remove skip_clean :all
This has been a no-op since
Homebrew/homebrew@c87736e7b9ded6ccef805f807d5844a1e948c3cc.
mathgl: remove BuildOptions monkeypatch
Only the interface exposed via the `build` attribute is public. The
BuildOptions constant itself is an implementation detail.
Stop using class-level build.stable?, build.devel?, and build.head?
Using these methods in the class body will soon emit a deprecation
warning (only in the class body, they will continue to be supported in
instance methods).
pbsuite 14.7.14
sspace-longread 1-1
SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs
using long reads (e.g. PacBio RS reads). Using the long read information,
contigs (or scaffolds) are placed in the right order and orientation in
so-called super-scaffolds.
platanus: use gcc opt_lib
opencv: add gstreamer, quicktime options
Recommend OpenEXR for interoperability.
Closes #951.
corset 1.02 (new formula)
Closes #1138.
cerulean 0.1: New formula
Cerulean extends contigs assembled using short read datasets like Illumina
paired-end reads using long reads like PacBio RS long reads.
update vips,rb to 7.40.6
- fix similarity rotate+scale
- fix 16-bit PNG save
- fix vipsthumbnail on many-core systems
Closes #1140.
vips: style cleanup
abyss-explorer: add doi, tag
ucsc-genome-browser 304
lumpy-sv: update to 0.2.7, remove Perl dependency
Closes #1144.
Move OpenFST, OpenGRM-ngram, and OpenGRM-thrax from core
As per the discussion in
https://github.com/Homebrew/homebrew/pull/31888, the maintainers feel
that homebrew-science is the right place for OpenFST and OpenGRM. I have
moved two homebrew formulae here (openfst and opengrm-ngram) as well as
a new one, opengrm-thrax, which also depends on OpenFST.
OpenGRM-thrax is a tool for compiling morphological analyzers and
context-sensitive rewrite rules into OpenFST automata.
Closes #1146.
Signed-off-by: Jack Nagel <jacknagel@gmail.com>
primer3: add primer3_config
Closes #1143.
adam 0.13.0 (new formula)
ADAM is a JVM based system for processing genomic data. ADAM runs
on the Apache Spark computing framework and can run both locally
and distributed across a cluster.
Closes #1142.
root 5.34.20
Closes #1155.
lp_solve: fix audit warning
Use NumpyHasHeaders over LanguageModuleDependency.
graph-tool: use Python module deps
Closes #1134.
openblas 0.2.11
lp_solve: fix typo
viennarna 2.1.8
pymol 1.7.2.1
astrometry-net 0.50
Fixes #1139.
Data-science-toolbox: update sha1.
Fixes #1160.
nextflow 0.10.0
Closes #1164.
mbsystem 5.4.2202
Closes #1165.
opencv: add libdc1394 as optional dependency
Closes #1167.
spades 3.1.1
swrcfit 1.3 (new formula)
Closes #1161.
Nexusformat: adding recommended hdf4 dependency
Closes #1166.
vips 7.40.8
Includes fix for jcupitt/libvips#172.
Closes #1172.
openni2: fix patch shasum
Closes #1169.
edirect 2.00
proverif 1.88.1 (new formula)
Closes #1168.
edirect: Update sha1
edirect: Add tag
picard-tools 1.120
Closes #1184.
seqtk/tabtk: Update and move tabtk to separate build
The latest seqtk GitHub moves tabtk to its own repo, breaking HEAD
(chapmanb/bcbio-nextgen#592). This creates separate builds for both,
fixes the tabtk issue, and moves to GitHub versioning of seqtk/tabtk
since it doesn't have a formal release process.
Closes #1183.
abyss: Add bioinformatics tag
pbsuite: Add dependency on blasr and python
Add bioinformatics tag and the DOI for PBHoney.
abyss: Run make check and add --without-check
edirect: update sha1
pcl 1.7.2 (new formula)
Closes #1181.
paml 4.8a
pear 0.9.5
wcstools 3.9.0
tbl2asn 23.7
cantera 2.1.2
Closes #1186.
bedtools 2.21.0
asl 20140826
Closes #1187.
r: append LDFLAGS for openblas and gettext
Fixes #829.
nextflow 0.10.1
Closes #1176.
Explicit link to libreadline.
Fixes #1150.
r-gui 1.65
- Updated to new version (1.65).
- Removed unnecessary patch.
Closes #1188.
pcl: fix apps install path
Closes #1189.
seqtk 1.0
prodigal 2.6.1
ssake 3.8.2: New formula
SSAKE is a de novo assembler for short DNA sequence reads.
ogdraw: Add DOI and tag
ogdraw: Set PERL5LIB in the test
ogdraw: Do not install perllocal.pod
Use make pure_install rather than make install.
ogdraw: Install irscan
drawgenemap: Add --irscan and --ircoord options
ogdraw: Fix the test
ncl 2.1.18 (new formula)
NEXUS Class Library is a C++ library for parsing NEXUS files.
seqtk 1.0-r68
Reverts f7986f3.
vtk: add qt5 support
Closes #1194.
vips 7.40.9
Closes #1198.
samtools 1.0
htslib 1.1
samtools 1.1
bcftools 1.1
tabtk 2014-09-22-r9
pcl: Add HEAD support
Closes #1197.
tabtk: fix r9 url
exonerate 2.4.0 devel
Zoltan 3.8: graph partitioning and load balancing
Closes #1192.
tasr 1.5.1: New formula
TASR is a genomics application that allows hypothesis-based interrogation of
genomic regions (sequence targets) of interest. It only considers NGS reads
for assembly that have overlap potential to input sequence targets.
Closes #1195
hlaminer 1.1: New formula
HLAminer is a software for HLA class I and II predictions from next-generation
shotgun (NGS) sequence read data that supports direct read alignment and
targeted assembly of sequence reads.
Closes #1196
ssake: update sha1
Closes #1202.
tasr 1.5.1: Update the URL
Closes #1204
abyss 1.5.2: Fix gtest
Use boost-python instead of boost => with-python
Boost.Python support in Homebrew is moving from the boost formula to a
new boost-python formula. This commit updates formulas that were using
boost --with-python to use boost-python instead.
This should not be committed to master until homebrew/homebrew#30957 is
accepted.
Closes #1080.
pcl: Disable cloud_composer and point_cloud_editor
Qt4 apps are not compatible with boost 1.56, and PCL is not ready
to switch to Qt5 yet.
Fixes #1209.
Closes #1211.
hlaminer: Add dependency to blast
Closes #1206.
vips 7.40.10
Closes #1213.
methpipe 3.3.1 (new formula)
Closes #1207.
ASL: version 20140929.
edirect 2.00: Update SHA1
Was 7f30f659f58c4bb77b87e514042fd415d226fc9a
Now c77a311486816966456712b2117503fea4aaa1a8
maker 2.31.5: repeatmasker, snap are recommended
Depends on DBD::Pg
Fix Inline::C dependency
maker 2.31.5: DBD::Pg is optional
maker 2.31.6
ogdraw 1.1.1: Add patch for --gc option
gdcm 2.4.4
Closes #1212.
tophat 2.0.13
Closes #1223.
nextflow 0.10.3
Closes #1224.
ASL: 20141003
Fixes #1227.
veclibfort: update to 0.4.2
vecLibFort now works with Leopard, even PPC Leopard. This has been accomplished without breaking compatibility with newer versions of OSX.
Closes #1232.
opencv: fix CUDA support
Closes #1228.
Closes #970.
Fixes #1182.
mrbayes: comment out ENV setting with mpi
open-mpi has been updated to 1.8, which doesn't use llvm-gcc to do
compiling the comment about the hang doesn't apply anymore.
Closes #1226.
ASL: 20141004
Closes #1237.
osgearth: build open-scene-graph with Qt
Fixes #1238.
edirect: update sha1
vips 7.40.11
Closes #1239.
fsa 1.15.9: New formula
FSA is a probabilistic multiple sequence alignment algorithm which uses a
distance-based approach to aligning homologous protein, RNA or DNA sequences.
blast 2.2.29: Fails to build with clang build 600
Closes #1078
pcl: add patch for boost 1.56
Enables cloud_composer and point_cloud_editor
Using WITH_QT to disable qt support
Closes #1241.
octave: build with clang 3.5
Fixes #1193.
Closes #1246.
bowtie 1.1.1
Closes #1245.
root 5.34.22
Closes #1247.
New formula: cvblob
Closes #1225.
exonerate 2.2.0: Fix undefined reference error
ssake: update sha1
Closes #1260.
tasr: update sha1
Closes #1259.
hlaminer: update sha1
Closes #1258.
r: Link libraries, headers, & frameworks
Link headers, libraries, & framework into normal locations on OS X
to allow other software to easily find them implicitly rather than
needing an explicit path upon compilation.
Prefer install_symlink over ln_s
Closes #1261.
octave: use opt lib path
openblas 0.2.12
Updates 0.2.11 to 0.2.12 and addresses issue #1157
Closes #1265.
sga 0.10.13: Install scripts
amos: fix Perl module dependency, cleanup
Bump clang version
Check configure args against build.with?
Fixes #1254.
insighttoolkit 4.6.1
Closes #1273.
nextflow 0.10.3: Add post_install
Run nextflow -download in post_install.
prokka 1.10: Depends on XML::Simple
vtk: modernize options
CONTRIBUTING: update gist-logs usage
sbagen 1.4.5 (new formula)
Closes #1266.
root: link against up-to-date OpenSSL
System OpenSSL is deprecated.
swetest: update resource sha1
Closes #1278.
clustal-w: bump clang, use double quotes
Closes #1281.
edirect: update sha1
root: general cleanup
Closes #1283.
octave: build gnuplot with Qt
Fixes #1275.
CONTRIBUTING: update core doc links
README: migrate from core wiki
mrbayes 3.2.3
MrBayes is updated to version 3.2.3 on SourceForge
https://sourceforge.net/projects/mrbayes/files/mrbayes/3.2.3/
Closes #1288.
Alglib: numerical analysis and data processing library
Closes #1177.
getdp: Update sha1.
Closes #1300.
Sundials: update url.
The official Sundials site requires registration and doesn't provide
a direct download link any more.
Arpack: Use MPI compilers.
Closes #1294.
masurca 2.2.1: conflicts with jellyfish, parallel
cuba 4.0
Closes #1305.
netcdf: update fortran resource to 4.4.1
Closes #1301.
Armadillo 4.500.0
Closes #1310.
ASL: version 20141024.
Closes #1309.
blis: new formula
BLIS - BLAS-like Library Instantiation Software
BLIS is a software framework for instantiating
high-performance BLAS-like dense linear algebra libraries.
The formula currently requires a "--with-configuration" option to
specify the framework configuration and raises an error if this option
is not specified.
Signed-off-by: Kevin Locke <kevin@kevinlocke.name>
Closes #1097.
Superlu_dist 3.3 (new formula)
Distributed version of SuperLU
Closes #1296.
sga 0.10.13: Install sga-align and sga-joinedpe
sga 0.10.13: Do not install Makefile Makefile.in
r 3.1.2
"Pumpkin Helmet" was released October 31, 2014.
See more: https://stat.ethz.ch/pipermail/r-announce/2014/000578.html
Closes #1315.
maker: remove optional module dep
:optional, :recommended are deprecated for modules.
cantera: remove outdated devel
mathomatic: fix audit warning
Convert devel to HEAD.
mrbayes: cleanup
qrupdate: use lower-case formula name
analysis: update homepage
opencv: make eigen recommended
Closes #1287.
osgearth: fix option precedence
octave: set GNUTERM in site octaverc
Avoid Octave's default gnuplot aquaterm graphics interface.
Set GNUTERM=qt with Octave's Qt-based GUI installed.
Closes #1308.
p4est: 1.1 (new formula)
Closes #1292.
ASL: 20141030.
Fixes #1322.
phylip 3.696
littler 0.2.1
sextractor 2.19.5
Also makes formula Yosemite-compatible
Closes #1321.
octave: ship the header file for building with octave source
Fixes #1289. Closes #1319.
PaStiX: version 5.2.2.18
Fix versioned library names.
Closes #1326.
bowtie2 2.2.4
Closes #1335.
r: Add an additional rJava caveat
To fix 'fatal error: 'jni.h' file not found' after running
'R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers'
as suggested
Closes #1330.
Correct uppercase name on veclibfort
Closes #1340.
New formula: statismo
Closes #1333.
ParaView 4.2.0: New formula
ParaView is an open-source, data analysis and visualization application.
Closes #1244.
ASL: version 20141106.
Closes #1343.
stacks 1.21
Depends on htslib rather than samtools for BAM support.
stacks 1.21: Remove --disable-openmp
It is not necessary to use --disable-openmp with clang 6.0.
infernal 1.1.1: Add tag bioinformatics
qualimap: update to v2.0
Closes #1348.
sailfish 0.6.2: Fails to build with clang 600
Add bioinformatics tag.
jellyfish-1.1: fails with clang
Closes #1354.
bedtools 2.22.0
Closes #1351.
sailfish 0.6.3
Bump fails_with clang
Closes #1355.
zoltan 3.81
New version of Zoltan (3.81).
Closes #1349.
gdcm: add option to build with vtk
Closes #1331.
gdcm: add c++11 option
Closes #1356.
insighttoolkit: add option to build ITK with gdcm
Closes #1332.
gromacs: deprecate options
netcdf: deprecate option
cmor: update netcdf option
edirect: update sha1
infernal: update check option
paraview: general cleanup
parmetis: general cleanup
"universal" is automatically passed to dependencies
Optional resources do not need to be conditional
Resources are downloaded on-demand, so declarations don't need to be
wrapped in a conditional.
Petsc 3.5.2
Update PETSc to the newest version.
Add numerous dependencies (metis, parmetis, scalapack, mumps, superlu_dist)
and options (compex/real).
Closes #1298.
GetDP: stable incompatible with PETSc/SLEPc 3.5.2
- Temporarily fail if building stable against PETSc/SLEPc
- Update sha1
- Update PETSC_ARCH / SLEPC_ARCH.
TAO: delete formula.
TAO is now part of PETSc as of version 3.5.2.
Slepc 3.5.2 (update)
Update SLEPc to the newest version.
Add optional dependency on Arpack.
Closes #1298.
Updates for Mountain Lion.
Harry 0.3.2: New formula
Harry is a tool for comparing strings and measuring their similarity. The tool
supports several classic string distances, such as the Levenshtein and
Jaro-Winkler distance, as well as modern string kernels, such as the Spectrum
and Subsequence kernel.
Closes #1364.
Sally 0.9.1: New formula
Sally is a tool for mapping a set of strings to a set of vectors. This mapping
is referred to as embedding and allows for applying techniques of machine
learning and data mining for analysis of string data.
Closes #1365.
Crlibm: new formula
Closes #1362.
Harry: Add support for head
Closes #1367.
Sally: Add support for head
Closes #1368.
Libctl: New formula
Closes #1341.
ds9 7.3.2 (new formula)
Closes #1311.
repeatmasker, repeatmodeler, repeatscout: Add tag
Add tag bioinformatics
plink: Option to skip version webcheck
Closes #1363.
openimageio: make qt optional
qt dependency is optional OpenImageIO needs Qt only for its viewer.
Closes #1361.
delly: update to 0.6.1, avoid bundled bamtools/htslib
Closes #1370.
plink: style nits
openimageio: style nits
nauty: update option
flann: update options
flann: fix octave option
kat 1.0.6
New release (V1.0.6) and updated jellyfish dependency to 1.1.11.
Closes #1346.
New formula: SimpleITK
Closes #1303.
SISL 4.6.0 (new formula)
SISL is a NURBS (Non Uniform Rational B-Splines) software library developed and
maintained by the geometry modelling group at SINTEF ICT, Department of Applied
Mathematics.
Closes #1271.
Numdiff 5.8.1 (new formula)
A program that compares putatively similar files line by line and
field by field, ignoring small numeric differences or/and different
numeric formats.
Closes #1372.
nexusformat: version 4.3.3
Closes #1366.
kat 1.0.6: Add bioinformatics tag
repeatscout 1.0.5: Add optional dependency on trf
To filter your repeat library to remove low-complexity and tandem sequences,
you will neeed to have perl 5.5 (or better; see http://www.perl.com), nseg
(Wooton and Federhen, 1993; see ftp://ftp.ncbi.nih.gov/pub/seg/nseg) and trf
(Benson, 1999; see http://tandem.bu.edu/trf/trf.html).
See http://bix.ucsd.edu/repeatscout/README.txt
See #1338
Sally 0.9.2: New release
This release fixes a severe bug in the computation of blended n-grams.
Closes #1375.
New Formula: Dynare 4.4.3
Dynare is a software platform for handling a wide class of economic
models, in particular dynamic stochastic general equilibrium (DSGE) and
overlapping generations (OLG) models. The models solved by Dynare
include those relying on the rational expectations hypothesis, wherein
agents form their expectations about the future in a way consistent with
the model. But Dynare is also able to handle models where expectations
are formed differently: on one extreme, models where agents perfectly
anticipate the future; on the other extreme, models where agents have
limited rationality or imperfect knowledge of the state of the economy
and, hence, form their expectations through a learning process. In terms
of types of agents, models solved by Dynare can incorporate consumers,
productive firms, governments, monetary authorities, investors and
financial intermediaries. Some degree of heterogeneity can be achieved
by including several distinct classes of agents in each of the
aforementioned agent categories.
Closes #1106.
mfusg (new formula)
Closes #1230.
vtk5: update options
vtk: update options
nexusformat: add make check
Closes #1379.
blast 2.2.30
Builds with current gcc v4.9.2
Closes #1381.
blast: add mirror
moab: update sha1
augustus 3.0.1: Add DOI and tag
ASL: version 20141111.
Fixes #1392.
htsbox r266: New formula
blast 2.2.30: Fix /usr/bin/basename: No such file
Closes #1396
phylip: add doi & tag
viennarna: add doi & tag
clustal-w: add bioinformatics tag
clustal-omega: add doi
mrbayes: add doi & tag
hyphy 2.2.2
Closes #1388.
tbl2asn 23.9
Closes #1391.
new formula: libsigrokdecode 0.3.0
Closes #1251.
New formula: lighter 1.0.3
Closes #1389.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
lighter: add 1.0.3 bottle.
hdf5: update options
Closes #1403.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
hdf5: add 1.8.13 bottle.
blast: builds with clang
Closes #1383.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
blast: add 2.2.30 bottle.
new formula: sigrok-cli 0.5.0
Closes #1045.
root 5.34.23
Closes #1399.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
root: add 5.34.23 bottle.
sambamba: 0.5.0-alpha (new formula)
Closes #1398.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
sambamba: add 0.5.0 bottle.
Update hdf5 cxx options
fqzcomp 4.6: New formula
Closes #1390.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
fqzcomp: add 4.6 bottle.
new formula: pulseview-0.2.0
Closes #1047.
abyss 1.5.2: Change single quotes to double quotes
Closes #1404.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
abyss: add 1.5.2 bottle.
blast 2.2.30: Change SHA, and upstream fixed #1396
Closes #1407.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
blast: update 2.2.30 bottle.
quake 0.3.5: Needs OpenMP
Closes #1408.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
Flint: new formula
Closes #1411.
Maxima 5.34.1.
Closes #1405.
oce 0.16.1
Closes #1414.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
oce: add 0.16.1 bottle.
paml: fix incorrect SHA1 sum
Closes #1415.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
paml: add 4.8a bottle.
root 5.34.24
Closes #1416.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
root: update 5.34.24 bottle.
hdf5 1.8.14
Closes #1420.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
hdf5: update 1.8.14 bottle.
abyss: modernize autotools deps
adol-c: modernize autotools deps
beagle: modernize autotools deps
fastx_toolkit: modernize autotools deps
hmmer: modernize autotools deps
minc: modernize autotools deps
moab: modernize autotools deps
mrbayes: modernize autotools deps
openni: modernize autotools deps
sga: modernize autotools deps
snp_sites: modernize autotools deps
z3: modernize autotools deps
emboss: modernize deps
enblend-enfuse: modernize deps
h5utils: modernize deps
insighttoolkit: modernize deps
mathgl: modernize deps
opencv: modernize deps
paraview: modernize deps
pocl: modernize deps
pymol: modernize deps
therion: modernize deps
ucsc-genome-browser: modernize deps
vigra: modernize deps
vips: modernize deps
vtk: modernize deps
vtk5: modernize deps
root: update Qt support
Fixes #1426.
hdf5: add make check
Closes #1421.
xbyak 4.70 (new formula)
Closes #1413.
ate-pairing 1.0 (new formula)
Closes #1413.
lobstr 3.0.3 (new formula)
lobSTR: A short tandem repeat profiler for personal genomes
http://genome.cshlp.org/content/early/2012/04/19/gr.135780.111.abstract
Closes #1424.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
asl 20141202
Fixes #1427.
abyss 1.5.2: Fix --enable-maxk and make default 96
Closes #1423.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
abyss: update 1.5.2 bottle.
lobstr: modernize autotools deps
opencv: Add --with-opengl option
Closes #1336.
emboss: expand options
Closes #1430.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
emboss: add 6.6.0 bottle.
armadillo 4.550.2
Closes #1431.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
armadillo: add 4.550.2 bottle.
r: update bash completion
Closes #1433.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
r: add 3.1.2 bottle.
netcdf: update options
Closes #1434.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
netcdf: add 4.3.2 bottle.
kraken: simplify fails_with clang
beetl: simplify fails_with
samblaster 0.1.20 (new formula)
Closes #1397.
flint: add doi
Closes #1425.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
flint: add 2.4.4 bottle.
pspp 0.8.4
Closes #1214.
radx 20141123
Closes #1436.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
radx: add 20141123 bottle.
netcdf: bump revision because main dependency (hdf5) has been updated
Closes #1437.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
netcdf: update 4.3.2_1 bottle.
r 3.1.2: Fix LDFLAGS for Linuxbrew
If LDFLAGS contains any -L options, configure sets LD_LIBRARY_PATH to
search those directories. Remove -LHOMEBREW_PREFIX/lib from LDFLAGS.
Revision hdf5 deps with versioned links
Most downstream formulae link against libhdf5.x.dylib instead of the
stable libhdf5.dylib symlink.
Closes #1441.
Signed-off-by: Ian Lancaster <ilancaster@gmail.com>
cdo: add 1.6.3_1 bottle.
field3d: add 1.4.3_1 bottle.
h5utils: add 1.12.1_1 bottle.
insighttoolkit: add 4.6.1_1 bottle.
minc: add 2.1.13_1 bottle.
openimageio: add 1.4.8_1 bottle.
seqdb: add 0.2.0_1 bottle.
shogun: add 2.1.0_1 bottle.
vtk5: add 5.10.1_1 bottle.
vtk: add 6.1.0_1 bottle.
itsol: migrate from core
salt: migrate from core
Use official API for disabling shallow clones
Optional resources do not need to be conditional
Resources are downloaded on-demand, so declarations don't need to be
wrapped in a conditional.
libsigrokdecode: only append to PKG_CONFIG_PATH once
`lib` is the same inside or outside of a resource("...").stage block.
Avoid "build.head?" in the DSL
Fewer conditionals in the class body
maker 2.31.6: Add option --with-postgresql
maker 2.31.6: Optionally configure MAKER for MPI
maker 2.31.6: Add bioinformatics tag
maker 2.31.7
maker 2.31.8
Closes #1450.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
fasta 36.3.7
Closes #1417.
Signed-off-by: Shaun Jackman <sjackman@gmail.com>
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I'm getting the following error with VarScan:
Looking at the
bcbio-nextgen-commands.logthe calls to snpeff are different for the other tools:The text was updated successfully, but these errors were encountered: