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_protvis(env):
""" Installs Andrew Brock's proteomics visualize tool.
https://bitbucket.org/Andrew_Brock/proteomics-visualise/
"""
_setup_protvis_env(env)
default_revision = "8cc6af1c492c"
protvis_home = env["protvis_home"]
revision = env.get("protvis_revision", default_revision)
url = _get_bitbucket_download_url(revision, "https://bitbucket.org/Andrew_Brock/proteomics-visualise")
galaxy_data_dir = env.get('galaxy_data_dir', "/mnt/galaxyData/")
protvis_converted_files_dir = env.get('protvis_converted_files_dir')
env.safe_sudo("sudo apt-get -y --force-yes install libxml2-dev libxslt-dev")
def _make(env):
env.safe_sudo("rsync -avur --delete-after . %s" % (protvis_home))
_chown_galaxy(env, protvis_home)
with cd(protvis_home):
env.safe_sudo("./setup.sh", user=env.get("galaxy_user", "galaxy"))
_get_install(url, env, _make)
_write_to_file('''GALAXY_ROOT = "%s"
PATH_WHITELIST = ["%s/files/", "%s"]
CONVERTED_FILES = "%s"
''' % (env.galaxy_home, galaxy_data_dir, protvis_converted_files_dir, protvis_converted_files_dir), "%s/conf.py" % protvis_home, 0755)
_setup_protvis_service(env)
def install_gmap(env):
"""GMAP and GSNAP: A Genomic Mapping and Alignment Program for mRNA EST and short reads.
http://research-pub.gene.com/gmap/
"""
version = "2012-11-09"
url = "http://research-pub.gene.com/gmap/src/gmap-gsnap-%s.tar.gz" % version
_get_install(url, env, _configure_make)
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_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 = "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_transproteomic_pipeline(env):
"""
"""
## version should be of form X.X.X-codename
default_version = "4.6.2-occupy"
version = env.get("tool_version", default_version)
version_parts = re.match("(\d\.\d)\.(\d)-(.*)", version)
major_version = version_parts.group(1)
revision = version_parts.group(2)
codename = version_parts.group(3)
if revision == "0":
download_rev = ""
else:
download_rev = ".%s" % revision
download_version = ("%s%s" % (major_version, download_rev))
url_pieces = (major_version, codename, revision, download_version)
url = 'http://sourceforge.net/projects/sashimi/files/Trans-Proteomic Pipeline (TPP)/TPP v%s (%s) rev %s/TPP-%s.tgz' % url_pieces
#install_dir = os.path.join(env["system_install"], "bin")
def _chdir_src(work_cmd):
def do_work(env):
with cd("src"):
append("Makefile.config.incl", "TPP_ROOT=%s/" % env["system_install"])
append("Makefile.config.incl", "TPP_WEB=/tpp/")
append("Makefile.config.incl", "XSLT_PROC=/usr/bin/xsltproc")
append("Makefile.config.incl", "CGI_USERS_DIR=${TPP_ROOT}cgi-bin")
work_cmd(env)
return do_work
def _make(env):
run("make")
env.safe_sudo("make install")
_get_install(url, env, _chdir_src(_make))
def install_macs(env):
"""Model-based Analysis for ChIP-Seq.
http://liulab.dfci.harvard.edu/MACS/
"""
version = "1.4.2"
url = "https://github.com/downloads/taoliu/MACS/" "MACS-%s.tar.gz" % version
_get_install(url, env, _python_make)
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_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_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_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_s3fs(env):
"""FUSE-based file system backed by Amazon S3.
https://code.google.com/p/s3fs/
"""
version = "1.61"
url = "http://s3fs.googlecode.com/files/s3fs-{0}.tar.gz".format(version)
_get_install(url, env, _configure_make)
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_varianttools(env):
version = "1.0.1"
version_ext = "a"
url = "http://downloads.sourceforge.net/project/varianttools/" "{ver}/variant_tools-{ver}{ext}.tar.gz".format(
ver=version, ext=version_ext
)
_get_install(url, env, _python_make)
def install_gnu_parallel(env):
"""GNU parallel: build and execute command lines from standard input in parallel.
https://savannah.gnu.org/projects/parallel/
"""
version = "20130122"
url = "ftp://ftp.gnu.org/gnu/parallel/parallel-%s.tar.bz2" % version
_get_install(url, env, _configure_make)
def install_samtools(env):
"""SAM Tools provide various utilities for manipulating alignments in the SAM format.
http://samtools.sourceforge.net/
"""
default_version = "0.1.19"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env, "samtools", version, stdout_flag="Version:"):
env.logger.info("samtools version {0} is up to date; not installing"
.format(version))
return
url = "http://downloads.sourceforge.net/project/samtools/samtools/" \
"%s/samtools-%s.tar.bz2" % (version, version)
def _safe_ncurses_make(env):
"""Combine samtools, removing ncurses refs if not present on system.
"""
with settings(warn_only=True):
result = env.safe_run("make")
# no ncurses, fix Makefile and rebuild
if result.failed:
env.safe_sed("Makefile", "-D_CURSES_LIB=1", "-D_CURSES_LIB=0")
env.safe_sed("Makefile", "-lcurses", "# -lcurses")
env.safe_run("make clean")
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
for fname in env.safe_run_output("ls -1 samtools bcftools/bcftools bcftools/vcfutils.pl misc/wgsim").split("\n"):
env.safe_sudo("cp -f %s %s" % (fname.rstrip("\r"), install_dir))
_get_install(url, env, _safe_ncurses_make)
def install_abyss(env):
# XXX check for no sparehash on non-ubuntu systems
version = "1.2.7"
url = "http://www.bcgsc.ca/downloads/abyss/abyss-%s.tar.gz" % version
def _remove_werror(env):
sed("configure", " -Werror", "")
_get_install(url, env, _configure_make, post_unpack_fn=_remove_werror)
def install_bx_python(env):
"""Tools for manipulating biological data, particularly multiple sequence alignments
https://bitbucket.org/james_taylor/bx-python/wiki/Home
"""
version = "bitbucket"
url = "hg clone http://bitbucket.org/james_taylor/bx-python"
_get_install(url, env, _python_make)
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_gatk(env):
"""GATK-lite: library for writing efficient analysis tools using next-generation sequencing data
http://www.broadinstitute.org/gatk/
"""
# Install main gatk executable
version = "2.3-9-gdcdccbb"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTKLite-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
# Install R gsalib for report and pdf generation
# XXX Currently have issues with gsalib R installation.
# Need to make this into a proper R package and re-enable
if False:
with quiet():
have_gsalib = env.safe_run("Rscript -e '\"gsalib\" %in% installed.packages()'")
if have_gsalib and "FALSE" in have_gsalib:
# install dependencies for gsalib
rlib_config = get_config_file(env, "r-libs.yaml").base
with open(rlib_config) as in_handle:
config = yaml.load(in_handle)
config["bioc"] = []
config["update_packages"] = False
config["cran"] = ["ggplot2", "gplots"]
libraries.r_library_installer(config)
# install gsalib
git_repo = "git clone --depth 1 https://github.com/broadgsa/gatk.git"
def install_gsalib(env):
env.safe_sudo("ant gsalib")
_get_install(git_repo, env, install_gsalib)
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_stacks(env):
"""Stacks: build loci out of a set of short-read sequenced samples.
http://creskolab.uoregon.edu/stacks/
"""
version = "0.998"
url = "http://creskolab.uoregon.edu/stacks/source/" "stacks-{0}.tar.gz".format(version)
_get_install(url, env, _configure_make)
def _install_boost(env):
version = "1.49.0"
url = "http://downloads.sourceforge.net/project/boost/boost" "/%s/boost_%s.tar.bz2" % (
version,
version.replace(".", "_"),
)
check_version = "_".join(version.split(".")[:2])
boost_dir = os.path.join(env.system_install, "boost")
boost_version_file = os.path.join(boost_dir, "include", "boost", "version.hpp")
def _boost_build(env):
run("./bootstrap.sh --prefix=%s --with-libraries=thread" % boost_dir)
run("./b2")
env.safe_sudo("./b2 install")
thread_lib = "libboost_thread.so.%s" % version
final_thread_lib = os.path.join(env.system_install, "lib", thread_lib)
if (
not exists(boost_version_file)
or not contains(boost_version_file, check_version)
or not exists(final_thread_lib)
):
_get_install(url, env, _boost_build)
orig_lib = os.path.join(boost_dir, "lib", thread_lib)
if not exists(final_thread_lib):
env.safe_sudo("ln -s %s %s" % (orig_lib, final_thread_lib))
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_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_varianttools(env):
"""Annotation, selection, and analysis of variants in the context of next-gen sequencing analysis.
http://varianttools.sourceforge.net/
"""
version = "1.0.6"
url = "http://downloads.sourceforge.net/project/varianttools/" \
"{ver}/variant_tools-{ver}-src.tar.gz".format(ver=version)
_get_install(url, env, _python_make)
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_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_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_delly(env):
"""DELLY: Structural variant discovery by integrated paired-end and split-read analysis
http://www.embl.de/~rausch/delly.html
"""
version = "0.0.11"
if versioncheck.up_to_date(env, "delly", version, stdout_flag="Deletion finder"):
return
url = "http://www.embl.de/~rausch/delly_v%s.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f",
do_make=False))
def install_emboss(env):
"""EMBOSS: A high-quality package of free, Open Source software for molecular biology.
http://emboss.sourceforge.net/
Emboss target for platforms without packages (CentOS -- rpm systems).
"""
default_version = "6.6.0"
version = env.get("tool_version", default_version)
url = "https://science-annex.org/pub/emboss/EMBOSS-%s.tar.gz" % version
#url = "ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-%s.tar.gz" % version
_get_install(url, env, _configure_make)
def SRC_install_cufflinks(env):
"""Cufflinks assembles transcripts and tests for differential expression and regulation in RNA-Seq samples.
http://cufflinks.cbcb.umd.edu/
"""
_install_samtools_libs(env)
_install_boost(env)
default_version = "2.0.2"
version = env.get("tool_version", default_version)
url = "http://cufflinks.cbcb.umd.edu/downloads/cufflinks-%s.tar.gz" % version
_get_install(url, env, _cufflinks_configure_make)
def SRC_install_tophat(env):
"""TopHat is a fast splice junction mapper for RNA-Seq reads
http://tophat.cbcb.umd.edu/
"""
_install_samtools_libs(env)
_install_boost(env)
default_version = "2.0.7"
version = env.get("tool_version", default_version)
url = "http://tophat.cbcb.umd.edu/downloads/tophat-%s.tar.gz" % version
_get_install(url, env, _cufflinks_configure_make)
def install_tophat(env):
"""TopHat is a fast splice junction mapper for RNA-Seq reads
http://tophat.cbcb.umd.edu/
"""
default_version = "2.0.8b"
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_cufflinks(env):
"""Cufflinks assembles transcripts and tests for differential expression and regulation in RNA-Seq samples.
http://cufflinks.cbcb.umd.edu/
"""
default_version = "2.1.1"
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_vcftools(env):
version = "0.1.7"
url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
v=version)
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)
def install_freebayes(env):
"""Bayesian haplotype-based polymorphism discovery and genotyping.
https://github.com/ekg/freebayes
"""
version = "github"
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_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_fastx_toolkit(env):
version = "0.0.13"
gtext_version = "0.6"
url_base = "http://hannonlab.cshl.edu/fastx_toolkit/"
fastx_url = "%sfastx_toolkit-%s.tar.bz2" % (url_base, version)
gtext_url = "%slibgtextutils-%s.tar.bz2" % (url_base, gtext_version)
def _remove_werror(env):
sed("configure", " -Werror", "")
_get_install(gtext_url, env, _configure_make, post_unpack_fn=_remove_werror)
_get_install(fastx_url, env, _configure_make, post_unpack_fn=_remove_werror)
def install_star(env):
"""The STAR spliced short read aligner.
http://code.google.com/p/rna-star/
"""
default_version = "2.3.1z"
version = env.get("tool_version", default_version)
# Need latest alpha release to work around 13.04 compile error
# https://groups.google.com/forum/#!topic/rna-star/13S344Jknf4
url = "ftp://ftp2.cshl.edu/gingeraslab/tracks/STARrelease/Alpha/STAR_{version}.tgz"
_get_install(url.format(version=version), env,
_make_copy("find . -name 'STAR'"))
def install_bwa(env):
version = "0.5.9"
url = "http://downloads.sourceforge.net/project/bio-bwa/bwa-%s.tar.bz2" % (
version)
def _fix_makefile():
arch = run("uname -m")
# if not 64bit, remove the appropriate flag
if arch.find("x86_64") == -1:
run("sed -i.bak -r -e 's/-O2 -m64/-O2/g' Makefile")
_get_install(url, env, _make_copy("ls -1 bwa solid2fastq.pl qualfa2fq.pl",
_fix_makefile))
def install_plink_seq(env):
"""A toolset for working with human genetic variation data.
http://atgu.mgh.harvard.edu/plinkseq/
"""
version = "0.08"
url = "http://atgu.mgh.harvard.edu/plinkseq/dist/" \
"version-{v}/plinkseq-{v}-x86_64.tar.gz".format(v=version)
def _plink_copy(env):
for x in ["pseq"]:
env.safe_sudo("cp {0} {1}/bin".format(x, env.system_install))
_get_install(url, env, _plink_copy)
def install_abyss(env):
# XXX check for no sparehash on non-ubuntu systems
version = "1.3.1"
url = "http://www.bcgsc.ca/downloads/abyss/abyss-%s.tar.gz" % version
def _remove_werror_get_boost(env):
sed("configure", " -Werror", "")
# http://osdir.com/ml/abyss-users-science/2011-10/msg00108.html
run("wget http://downloads.sourceforge.net/project/boost/boost/1.47.0/boost_1_47_0.tar.bz2")
run("tar jxf boost_1_47_0.tar.bz2")
run("ln -s boost_1_47_0/boost boost")
_get_install(url, env, _configure_make, post_unpack_fn=_remove_werror_get_boost)
def install_velvet(env):
version = "1.1.06"
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
"""
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_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_bfast(env):
"""BFAST: Blat-like Fast Accurate Search Tool.
http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page
"""
default_version = "0.7.0a"
version = env.get("tool_version", default_version)
major_version_regex = "\d+\.\d+\.\d+"
major_version = re.search(major_version_regex, version).group(0)
url = "http://downloads.sourceforge.net/project/bfast/bfast/%s/bfast-%s.tar.gz"\
% (major_version, version)
_get_install(url, env, _configure_make)
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_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_mosaik(env):
"""MOSAIK: reference-guided aligner for next-generation sequencing technologies
http://code.google.com/p/mosaik-aligner/
"""
version = "github"
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_perm(env):
version = "3.6"
url = "http://perm.googlecode.com/files/PerM_%s_Source.tar.gz" % version
def gcc44_makefile_patch():
gcc_cmd = "g++44"
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True):
result = run("%s -v" % gcc_cmd)
print result.return_code
if result.return_code == 0:
sed("makefile", "g\+\+", gcc_cmd)
_get_install(url, env, _make_copy("ls -1 perm", gcc44_makefile_patch))
def install_bedtools(env):
"""A flexible suite of utilities for comparing genomic features.
https://code.google.com/p/bedtools/
"""
version = "2.17.0"
if versioncheck.up_to_date(env,
"bedtools --version",
version,
stdout_flag="bedtools"):
return
url = "https://bedtools.googlecode.com/files/" \
"BEDTools.v%s.tar.gz" % version
_get_install(url, env, _make_copy("ls -1 bin/*"))
def install_dwgsim(env):
version = "0.1.8"
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):
run("wget {0}".format(samtools_url))
run("tar jxf samtools-{0}.tar.bz2".format(samtools_version))
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_samtools_libs(env):
repository = "svn co --non-interactive " \
"https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools"
def _samtools_lib_install(env):
lib_dir = _get_lib_dir(env)
include_dir = os.path.join(env.system_install, "include", "bam")
env.safe_run("make")
env.safe_sudo("mv -f libbam* %s" % lib_dir)
env.safe_sudo("mkdir -p %s" % include_dir)
env.safe_sudo("mv -f *.h %s" % include_dir)
check_dir = os.path.join(_get_include_dir(env), "bam")
if not env.safe_exists(check_dir):
_get_install(repository, env, _samtools_lib_install)
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):
env.safe_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_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_percolator(env):
default_version = "2_04"
version = env.get("tool_version", default_version)
url = "https://github.com/downloads/percolator/percolator/percolator_%s_full_src.tar.gz" % version
def make(env):
with cd(".."):
run("env")
run("cmake -DCMAKE_INSTALL_PREFIX='%s' . " % env.system_install)
run("make -j8")
env.safe_sudo("make install")
_get_install(url, env, make)