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bedtools: update to version 2.19.1 #742

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@iml iml added a commit that closed this pull request
@lparsons lparsons bedtools 2.19.1
Closes #742.
49ee9cc
@iml iml closed this in 49ee9cc
@lmrodriguezr lmrodriguezr added a commit to lmrodriguezr/homebrew-science that referenced this pull request
@lmrodriguezr lmrodriguezr Velvet make updated
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>

f…
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Commits on Mar 12, 2014
  1. @lparsons
Showing with 2 additions and 2 deletions.
  1. +2 −2 bedtools.rb
View
4 bedtools.rb
@@ -2,8 +2,8 @@
class Bedtools < Formula
homepage 'https://github.com/arq5x/bedtools2'
- url 'https://github.com/arq5x/bedtools2/releases/download/v2.19.0/bedtools-2.19.0.tar.gz'
- sha1 'f870c801ccc96a032f061db4d4a0c54f3ab46e64'
+ url 'https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz'
+ sha1 '7a9027d7992ae399cde8fb7dab520b332605740c'
head 'https://github.com/arq5x/bedtools2.git'
def install
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