def install_lumpy(env):
"""a general probabilistic framework for structural variant discovery
https://github.com/arq5x/lumpy-sv
"""
version = "github"
repository = "git clone git://github.com/arq5x/lumpy-sv.git"
_get_install(repository, env, _make_copy("ls -1 bin/*"))
_get_install(url, env, _make_copy("ls -1 bin/* scripts/*"), post_unpack_fn=clean_libs)
def install_echo(env):
"""ECHO: A reference-free short-read error correction algorithm
http://uc-echo.sourceforge.net/
"""
version = "1_11"
url = "http://downloads.sourceforge.net/project/uc-echo/source%20release/" "echo_v{0}.tgz".format(version)
_get_install_local(url, env, _make_copy())
def install_bowtie(env):
"""The bowtie short read aligner.
http://bowtie-bio.sourceforge.net/index.shtml
"""
version = "0.12.7"
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/%s/" "bowtie-%s-src.zip" % (version, version)
_get_install(url, env, _make_copy("find -perm -100 -name 'bowtie*'"))
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.sourceforge.net/
"""
version = "r2012-05-18"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" "trinityrnaseq_%s.tar.gz" % version
_get_install_local(url, env, _make_copy())
def install_bowtie2(env):
"""bowtie2 short read aligner, with gap support.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
version = "2.0.0-beta6"
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/%s/" "bowtie2-%s-source.zip" % (version, version)
_get_install(url, env, _make_copy("find -perm -100 -name 'bowtie2*'"))
def install_omssa(env):
print "Installing OMSSA"
default_version = "2.1.9"
version = env.get("tool_version", default_version)
url = 'ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/%s/omssa-%s.linux.tar.gz' % (version, version)
env.safe_sudo("mkdir -p '%s'" % env["system_install"])
_get_install(url, env, _make_copy(find_cmd="find -perm -100 -name 'omssa*'", do_make=False))
def install_lumpy(env):
"""a general probabilistic framework for structural variant discovery
https://github.com/arq5x/lumpy-sv
"""
version = "fca4706573"
repository = "git clone https://github.com/arq5x/lumpy-sv.git"
_get_install(repository, env, _make_copy("ls -1 bin/*"), revision=version)
def install_bedtools(env):
"""A flexible suite of utilities for comparing genomic features.
https://code.google.com/p/bedtools/
"""
version = "github"
repository = "git clone git://github.com/arq5x/bedtools.git"
_get_install(repository, env, _make_copy("ls -1 bin/*"))
def install_samtools(env):
"""SAM Tools provide various utilities for manipulating alignments in the SAM format.
http://samtools.sourceforge.net/
"""
version = "0.1.18"
url = "http://downloads.sourceforge.net/project/samtools/samtools/" "%s/samtools-%s.tar.bz2" % (version, version)
_get_install(url, env, _make_copy("find -perm -100 -type f"))
def install_tabix(env):
"""Generic indexer for TAB-delimited genome position files
http://samtools.sourceforge.net/tabix.shtml
"""
version = "0.2.6"
url = "http://downloads.sourceforge.net/project/samtools/tabix/tabix-%s.tar.bz2" % version
_get_install(url, env, _make_copy("ls -1 tabix bgzip"))
def install_mosaik(env):
"""MOSAIK: reference-guided aligner for next-generation sequencing technologies
http://code.google.com/p/mosaik-aligner/
"""
version = "2.1.73"
url = "http://mosaik-aligner.googlecode.com/files/" "MOSAIK-%s-binary.tar" % version
_get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))
def install_bedtools(env):
"""A flexible suite of utilities for comparing genomic features.
https://code.google.com/p/bedtools/
"""
version = "2.17.0"
url = "https://bedtools.googlecode.com/files/" "BEDTools.v%s.tar.gz" % version
_get_install(url, env, _make_copy("ls -1 bin/*"))
def install_snap(env):
"""Scalable Nucleotide Alignment Program
http://snap.cs.berkeley.edu/
"""
version = "0.15"
url = "http://github.com/downloads/amplab/snap/" "snap-%s-linux.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))
def install_freebayes(env):
repository = "git clone --recursive git://github.com/ekg/freebayes.git"
def _fix_library_order(env):
sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")
_get_install(repository, env, _make_copy("ls -1 bin/*"), post_unpack_fn=_fix_library_order)
def install_transabyss(env):
version = "1.2.0"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" "releases/%s/trans-ABySS-v%s.tar.gz" % (
version,
version,
)
_get_install_local(url, env, _make_copy(do_make=False))
def install_hydra(env):
version = "0.5.3"
url = "http://hydra-sv.googlecode.com/files/Hydra.v{0}.tar.gz".format(version)
def clean_libs(env):
run("make clean")
_get_install(url, env, _make_copy("ls -1 bin/* scripts/*"),
post_unpack_fn=clean_libs)
def install_cufflinks(env):
"""Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
http://cufflinks.cbcb.umd.edu/
"""
default_version = "2.0.2"
version = env.get("tool_version", default_version)
url = "http://cufflinks.cbcb.umd.edu/downloads/" "cufflinks-%s.Linux_x86_64.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))
def install_tophat(env):
"""TopHat is a fast splice junction mapper for RNA-Seq reads
http://tophat.cbcb.umd.edu/
"""
default_version = "2.0.7"
version = env.get("tool_version", default_version)
url = "http://tophat.cbcb.umd.edu/downloads/" "tophat-%s.Linux_x86_64.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))
def install_omssa(env):
default_version = "2.1.9"
version = env.get("tool_version", default_version)
url = 'ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/%s/omssa-%s.linux.tar.gz' % (version, version)
env.safe_sudo("mkdir -p '%s'" % env["system_install"])
## OMSSA really wants mods.xml, usermods.xml, etc... in the same directory
## so just copying everything there.
_get_install(url, env, _make_copy(find_cmd="ls -1", do_make=False))
def install_transabyss(env):
"""Analyze ABySS multi-k-assembled shotgun transcriptome data.
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
"""
version = "1.4.4"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" \
"releases/%s/trans-ABySS-v%s.tar.gz" % (version, version)
_get_install_local(url, env, _make_copy(do_make=False))
def install_bamutil(env):
"""Utilities for working with BAM files, from U of M Center for Statistical Genetics.
http://genome.sph.umich.edu/wiki/BamUtil
"""
version = "1.0.7"
url = "http://genome.sph.umich.edu/w/images/5/5d/BamUtilLibStatGen.%s.tgz" % version
_get_install(url, env, _make_copy("ls -1 bamUtil/bin/bam"),
dir_name="bamUtil_%s" % version)
def install_lastz(env):
version = "1.02.00"
url = "http://www.bx.psu.edu/miller_lab/dist/" "lastz-%s.tar.gz" % version
def _remove_werror(env):
sed("src/Makefile", " -Werror", "")
_get_install(url, env, _make_copy("find -perm -100 -name 'lastz'"), post_unpack_fn=_remove_werror)
def install_ogap(env):
"""gap opening realigner for BAM data streams
https://github.com/ekg/ogap
"""
version = "652c525"
repository = "git clone --recursive https://github.com/ekg/ogap.git"
_get_install(repository, env, _make_copy("ls ogap"),
revision=version)
def install_grabix(env):
"""a wee tool for random access into BGZF files
https://github.com/arq5x/grabix
"""
version = "fda4d2609"
repository = "git clone https://github.com/arq5x/grabix.git"
_get_install(repository, env, _make_copy("ls -1 grabix"),
revision=version)
def install_mosaik(env):
"""MOSAIK: reference-guided aligner for next-generation sequencing technologies
http://code.google.com/p/mosaik-aligner/
"""
version = "2.2.3"
url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/mosaik-aligner/" \
"MOSAIK-%s-Linux-x64.tar" % version
_get_install(url, env, _make_copy("find . -perm -100 -type f", do_make=False))
def install_mosaik(env):
repository = "git clone git://github.com/wanpinglee/MOSAIK.git"
def _chdir_src(work_cmd):
def do_work(env):
with cd("src"):
work_cmd(env)
return do_work
_get_install(repository, env, _chdir_src(_make_copy("ls -1 ../bin/*")))
def install_crisp(env):
version = "5"
url = "https://sites.google.com/site/vibansal/software/crisp/" "CRISP-linux-v{0}.tar.gz".format(version)
def _make_executable():
run("chmod a+x *.py")
_get_install(url, env, _make_copy("ls -1 CRISP.py crisp_to_vcf.py", premake_cmd=_make_executable, do_make=False))
def install_stampy(env):
"""Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
http://www.well.ox.ac.uk/project-stampy
"""
base_version = "1.0.15"
revision = "1360"
version = "{0}r{1}".format(base_version, revision)
url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" "stampy-{0}.tgz".format(version)
_get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))
def install_bowtie2(env):
"""bowtie2 short read aligner, with gap support.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
default_version = "2.1.0"
version = env.get("tool_version", default_version)
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/%s/" \
"bowtie2-%s-source.zip" % (version, version)
_get_install(url, env, _make_copy("find . -perm -100 -name 'bowtie2*'"))
def install_bowtie(env):
"""The bowtie short read aligner.
http://bowtie-bio.sourceforge.net/index.shtml
"""
default_version = "1.0.0"
version = env.get("tool_version", default_version)
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/%s/" \
"bowtie-%s-src.zip" % (version, version)
_get_install(url, env, _make_copy("find -perm -100 -name 'bowtie*'"))
def install_velvet(env):
"""Sequence assembler for very short reads.
http://www.ebi.ac.uk/~zerbino/velvet/
"""
default_version = "1.2.08"
version = env.get("tool_version", default_version)
url = "http://www.ebi.ac.uk/~zerbino/velvet/velvet_%s.tgz" % version
def _fix_library_order(env):
"""Fix library order problem in recent gcc versions
http://biostar.stackexchange.com/questions/13713/
error-installing-velvet-assembler-1-1-06-on-ubuntu-server
"""
env.safe_sed("Makefile", "Z_LIB_FILES=-lz", "Z_LIB_FILES=-lz -lm")
_get_install(url, env, _make_copy("find -perm -100 -name 'velvet*'"),
post_unpack_fn=_fix_library_order)
def install_ray(env):
"""Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sourceforge.net/
"""
default_version = "2.2.0"
version = env.get("tool_version", default_version)
url = "http://downloads.sourceforge.net/project/denovoassembler/Ray-v%s.tar.bz2" % version
def _ray_do_nothing(env):
return
_get_install(url,
env,
_make_copy("find . -name Ray"),
post_unpack_fn=_ray_do_nothing)
def install_freebayes(env):
"""Bayesian haplotype-based polymorphism discovery and genotyping.
https://github.com/ekg/freebayes
"""
version = "296a0fa"
repository = "git clone --recursive https://github.com/ekg/freebayes.git"
def _fix_tabixpp_library_order(env):
sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")
_get_install(repository,
env,
_make_copy("ls -1 bin/*"),
post_unpack_fn=_fix_tabixpp_library_order,
revision=version)
def install_weblogo(env):
"""Weblogo
http://weblogo.berkeley.edu/
"""
version = "2.8.2"
url = "http://weblogo.berkeley.edu/release/weblogo.%s.tar.gz" % version
_get_install(url, env,
_make_copy("find . -perm -100 -type f", do_make=False))
def _cp_pm(env):
for perl_module in ["template.pm", "logo.pm", "template.eps"]:
env.safe_sudo("cp %s %s/lib/perl5" %
(perl_module, env.system_install))
_get_install(url, env, _cp_pm(env))
def install_bwa(env):
"""BWA: aligns short nucleotide sequences against a long reference sequence.
http://bio-bwa.sourceforge.net/
"""
default_version = "0.7.4"
version = env.get("tool_version", default_version)
url = "http://downloads.sourceforge.net/project/bio-bwa/bwa-%s.tar.bz2" % (
version)
def _fix_makefile():
arch = env.safe_run_output("uname -m")
# if not 64bit, remove the appropriate flag
if arch.find("x86_64") == -1:
env.safe_run("sed -i.bak -r -e 's/-O2 -m64/-O2/g' Makefile")
_get_install(url, env, _make_copy("ls -1 bwa qualfa2fq.pl",
_fix_makefile))
def install_hydra(env):
"""Hydra detects structural variation breakpoints in both unique and duplicated genomic regions.
https://code.google.com/p/hydra-sv/
"""
version = "0.5.3"
url = "http://hydra-sv.googlecode.com/files/Hydra.v{0}.tar.gz".format(
version)
def clean_libs(env):
env.safe_run("make clean")
_get_install(url,
env,
_make_copy("ls -1 bin/* scripts/*"),
post_unpack_fn=clean_libs)
def install_superhirn(env):
default_version = "0.03"
version = env.get("tool_version", default_version)
url = "https://github.com/jmchilton/SuperHirn/zipball/%s/SuperHirn.zip" % version
def _chdir(work_cmd):
def do_work(env):
with cd("SuperHirnv03/make"):
work_cmd(env)
return do_work
_get_install(
url, env,
_chdir(_make_copy(find_cmd="find -perm -100 -name 'SuperHirn*'")))
def install_freec(env):
"""Control-FREEC: a tool for detection of copy number changes and allelic imbalances.
http://bioinfo-out.curie.fr/projects/freec/
"""
version = "6.4"
if env.distribution in ["ubuntu", "debian"]:
if env.is_64bit:
url = "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz"
else:
url = "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_LINUX32.tar.gz"
if not versioncheck.up_to_date(env, "freec", version, stdout_index=1):
_get_install(url,
env,
_make_copy("find . -name 'freec'"),
dir_name=".")
def install_vcflib(env):
"""Utilities for parsing and manipulating VCF files.
https://github.com/ekg/vcflib
"""
version = "06e664c"
repository = "git clone --recursive https://github.com/ekg/vcflib.git"
def _fix_tabixpp_library_order(env):
sed("tabixpp/Makefile", "-ltabix", "-ltabix -lz")
_get_install(repository,
env,
_make_copy("find -perm -100 -type f -name 'vcf*'"
" | grep -v '.sh$' | grep -v '.r$'"),
post_unpack_fn=_fix_tabixpp_library_order,
revision=version)
def install_lastz(env):
"""LASTZ sequence alignment program.
http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
"""
default_version = "1.02.00"
version = env.get("tool_version", default_version)
url = "http://www.bx.psu.edu/miller_lab/dist/" \
"lastz-%s.tar.gz" % version
def _remove_werror(env):
env.safe_sed("src/Makefile", " -Werror", "")
_get_install(url,
env,
_make_copy("find . -perm -100 -name 'lastz'"),
post_unpack_fn=_remove_werror)
def install_crisp(env):
"""Detect SNPs and short indels from pooled sequencing data.
https://sites.google.com/site/vibansal/software/crisp/
"""
version = "5"
url = "https://sites.google.com/site/vibansal/software/crisp/" \
"CRISP-linux-v{0}.tar.gz".format(version)
def _make_executable():
env.safe_run("chmod a+x *.py")
_get_install(
url, env,
_make_copy("ls -1 CRISP.py crisp_to_vcf.py",
premake_cmd=_make_executable,
do_make=False))
def install_perm(env):
"""Efficient mapping of short sequences accomplished with periodic full sensitive spaced seeds.
https://code.google.com/p/perm/
"""
default_version = "4"
version = env.get("tool_version", default_version)
url = "http://perm.googlecode.com/files/PerM%sSource.tar.gz" % version
def gcc44_makefile_patch():
gcc_cmd = "g++44"
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True):
result = env.safe_run("%s -v" % gcc_cmd)
print result.return_code
if result.return_code == 0:
env.safe_sed("makefile", "g\+\+", gcc_cmd)
_get_install(url, env, _make_copy("ls -1 perm", gcc44_makefile_patch))
def install_vcftools(env):
"""Work with VCF files, such as those generated by the 1000 Genomes Project.
http://vcftools.sourceforge.net/
"""
version = "0.1.11"
url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
v=version)
if versioncheck.up_to_date(env, "vcftools", version, stdout_flag="VCFtools"):
return
def _vcf_make(env):
env.safe_sudo("make install PREFIX={dir}".format(dir=env.system_install))
for perl_module in ["FaSlice.pm", "Vcf.pm", "VcfStats.pm"]:
env.safe_sudo("cp perl/%s %s/lib/perl5" % (perl_module, env.system_install))
env.safe_sudo("make clean")
_get_install(url, env, _vcf_make)
_get_install_local(url, env, _make_copy())
def install_dwgsim(env):
"""DWGSIM: simulating NGS data and evaluating mappings and variant calling.
http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page
"""
version = "0.1.10"
samtools_version = "0.1.18"
url = "http://downloads.sourceforge.net/project/dnaa/dwgsim/" \
"dwgsim-{0}.tar.gz".format(version)
samtools_url = "http://downloads.sourceforge.net/project/samtools/samtools/" \
"{ver}/samtools-{ver}.tar.bz2".format(ver=samtools_version)
def _get_samtools(env):
env.safe_run("wget {0}".format(samtools_url))
env.safe_run("tar jxf samtools-{0}.tar.bz2".format(samtools_version))
env.safe_run("ln -s samtools-{0} samtools".format(samtools_version))
_get_install(url, env, _make_copy("ls -1 dwgsim dwgsim_eval scripts/dwgsim_pileup_eval.pl"),
post_unpack_fn=_get_samtools)
def install_stampy(env):
"""Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
http://www.well.ox.ac.uk/project-stampy
"""
version = "1.0.21"
#version = base_version
#revision = "1654"
#version = "{0}r{1}".format(base_version, revision)
#url = "http://www.well.ox.ac.uk/bioinformatics/Software/" \
# "stampy-%s.tgz" % (version)
# Ugh -- Stampy now uses a 'Stampy-latest' download target
url = "http://www.well.ox.ac.uk/bioinformatics/Software/" \
"Stampy-latest.tgz"
def _clean_makefile(env):
env.safe_sed("makefile", " -Wl", "")
_get_install_local(url, env, _make_copy(),
dir_name="stampy-{0}".format(version),
post_unpack_fn=_clean_makefile)
def install_lumpy(env):
"""a general probabilistic framework for structural variant discovery
https://github.com/arq5x/lumpy-sv
"""
version = "0.1.2"
revision = "a8b9e14cc5"
if versioncheck.up_to_date(env, "lumpy", version, stdout_flag="Program:"):
return
repository = "git clone https://github.com/arq5x/lumpy-sv.git"
def _add_gsl_includes():
"""Add multi-environment include and library links for finding GNU Scientific Libraries.
"""
env.safe_sed("defs.local", "^\([^#]\)", "#\1")
env.safe_append("defs.local", ("GSL_INCLUDE=-I/usr/local/include -I/usr/local/include/gsl "
"-I/usr/include/gsl -I%s/include/gsl" % env.system_install))
env.safe_append("defs.local", ("GSL_LINK=-L/usr/local/lib -L/usr/lib -L%s/lib" % env.system_install))
_get_install(repository, env, _make_copy("ls -1 bin/*", _add_gsl_includes),
revision=revision)
def install_tophat(env):
"""TopHat is a fast splice junction mapper for RNA-Seq reads
http://tophat.cbcb.umd.edu/
"""
default_version = "2.0.9"
version = env.get("tool_version", default_version)
if versioncheck.is_version(env,
"tophat",
version,
args="--version",
stdout_flag="TopHat"):
env.logger.info(
"tophat version {0} is up to date; not installing".format(version))
return
platform = "OSX" if env.distribution == "macosx" else "Linux"
url = "http://tophat.cbcb.umd.edu/downloads/" \
"tophat-%s.%s_x86_64.tar.gz" % (version, platform)
_get_install(url, env,
_make_copy("find . -perm -100 -type f", do_make=False))
def install_freebayes(env):
"""Bayesian haplotype-based polymorphism discovery and genotyping.
https://github.com/ekg/freebayes
"""
version = "0.9.9.2-1"
revision = "c0cca0b5e"
if versioncheck.up_to_date(env, "freebayes", version, stdout_flag="version:"):
return
repository = "git clone --recursive https://github.com/ekg/freebayes.git"
def _fix_tabixpp_library_order(env):
env.safe_sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")
def _fix_autoversion(env):
env.safe_sed("src/Makefile", "all: autoversion ../bin/freebayes ../bin/bamleftalign",
"all: ../bin/freebayes ../bin/bamleftalign")
def _freebayes_fixes(env):
_fix_tabixpp_library_order(env)
_fix_autoversion(env)
_get_install(repository, env, _make_copy("ls -1 bin/*"),
post_unpack_fn=_freebayes_fixes,
revision=revision)
def install_featurecounts(env):
"""
featureCounts from the subread package for counting reads mapping to
genomic features
"""
default_version = "1.4.4"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env,
"featureCounts",
version,
stdout_flag="Version"):
return
platform = "MacOS" if env.distribution == "macosx" else "Linux"
url = ("http://downloads.sourceforge.net/project/subread/"
"subread-%s/subread-%s-%s-x86_64.tar.gz" %
(version, version, platform))
_get_install(
url, env,
_make_copy("find . -type f -perm -100 -name 'featureCounts'",
do_make=False))
def install_grabix(env):
"""a wee tool for random access into BGZF files
https://github.com/arq5x/grabix
"""
version = "0.1.2"
revision = "a78cbaf488"
try:
uptodate = versioncheck.up_to_date(env,
"grabix",
version,
stdout_flag="version:")
# Old versions will not have any version information
except IOError:
uptodate = False
if uptodate:
return
repository = "git clone https://github.com/arq5x/grabix.git"
_get_install(repository,
env,
_make_copy("ls -1 grabix"),
revision=revision)
def install_fido(env):
version = "2011"
url = 'http://noble.gs.washington.edu/proj/fido/fido.tar.gz'
# Adapted from Jorrit Boekel's mi-deployment fork
# https://bitbucket.org/glormph/mi-deployment-protoeimcs
def _chdir_src(work_cmd):
def do_work(env):
with cd("src/cpp"):
append('tmpmake', 'SHELL=/bin/bash')
append('tmpmake', 'prefix=%s' % env.get("system_install"))
append(
'tmpmake',
'CPPFLAGS=-Wall -ffast-math -march=x86-64 -pipe -O4 -g')
run('cat makefile |grep BINPATH -A 9999 >> tmpmake')
run('cp tmpmake makefile')
work_cmd(env)
return do_work
_get_install(
url, env,
_chdir_src(
_make_copy(find_cmd="find ../../bin -perm -100 -name 'Fido*'")))
def install_trinity(env):
version = "03122011"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
"trinityrnaseq-%s.tgz" % version
_get_install_local(url, env, _make_copy())
def install_samtools(env):
version = "0.1.17"
url = "http://downloads.sourceforge.net/project/samtools/samtools/" \
"%s/samtools-%s.tar.bz2" % (version, version)
_get_install(url, env, _make_copy("find -perm -100 -type f"))
def install_velvet(env):
version = "1.0.13"
url = "http://www.ebi.ac.uk/~zerbino/velvet/velvet_%s.tgz" % version
_get_install(url, env, _make_copy("find -perm -100 -name 'velvet*'"))
def install_bedtools(env):
repository = "git clone git://github.com/arq5x/bedtools.git"
_get_install(repository, env, _make_copy("ls -1 bin/*"))
def install_sabre(env):
repo = "git clone git://github.com/najoshi/sabre.git"
_get_install(repo, env, _make_copy("find -perm -100 -name 'sabre*'"))
def install_freebayes(env):
repository = "git clone --recursive git://github.com/ekg/freebayes.git"
_get_install(repository, env, _make_copy("ls -1 bin/*"))
def install_transabyss(env):
version = "1.2.0"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" \
"releases/%s/trans-ABySS-v%s.tar.gz" % (version, version)
_get_install_local(url, env, _make_copy(do_make=False))
def install_lastz(env):
version = "1.02.00"
url = "http://www.bx.psu.edu/miller_lab/dist/" \
"lastz-%s.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -name 'lastz'"))
def install_freebayes(env):
repository = "git clone --recursive git://github.com/ekg/freebayes.git"
def _fix_library_order(env):
sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")
_get_install(repository, env, _make_copy("ls -1 bin/*"),
post_unpack_fn=_fix_library_order)