def install_peptide_shaker(env):
default_version = "0.20.1"
version = env.get("tool_version", default_version)
url = "http://peptide-shaker.googlecode.com/files/PeptideShaker-%s.zip" % version
def install_fn(env, install_dir):
_get_gist_script(
env,
"https://gist.github.com/jmchilton/5002161/raw/f1fe76d6e6eed99a768ed0b9f41c2d0a6a4b24b7/PeptideShaker"
)
_get_gist_script(
env,
"https://gist.github.com/jmchilton/5002161/raw/8a17d5fb589984365284e55a98a455c2b47da54f/PeptideShakerCLI"
)
# Hack for multi-user environment.
env.safe_sudo("chmod -R o+w resources")
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = os.path.join(env.get("system_install"), "bin")
env.safe_sudo("mkdir -p '%s'" % bin_dir)
env.safe_sudo("ln -s '%s' %s" %
(os.path.join(install_dir, "PeptideShaker"),
os.path.join(bin_dir, "PeptideShaker")))
env.safe_sudo("ln -s '%s' %s" %
(os.path.join(install_dir, "PeptideShakerCLI"),
os.path.join(bin_dir, "PeptideShakerCLI")))
_java_install("PeptideShaker", version, url, env, install_fn)
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 = 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_gatk_protected(env):
"""Installation script for recent versions of GATK. Requires manual download from user.
http://www.broadinstitute.org/gatk/
"""
min_version = "2.7-2"
version = "%s-g6bda569" % min_version
dl_fname = "GenomeAnalysisTK-%s.tar.bz2" % min_version
with _make_tmp_dir() as work_dir:
work_fname = os.path.join(work_dir, dl_fname)
def manual_gatk_download(env):
print "**** Manual intervention needed"
print "Recent GATK versions require manual download from the GATK website"
print "Please retrieve the latest versions from:"
print "http://www.broadinstitute.org/gatk/download"
print "and place %s in your home directory" % dl_fname
userin = raw_input("**** Press <enter> when complete or type 'skip' to avoid the installation: ")
if userin.find("skip") >= 0:
return None
else:
try:
fname = env.safe_run_output("ls $HOME/%s" % dl_fname)
except:
raise IOError("Could not find %s in your home directory. Please download and retry" % dl_fname)
env.safe_put(fname, work_fname)
return work_fname
_java_install("gatk", version, work_fname, env, pre_fetch_fn=manual_gatk_download)
def install_picard(env):
"""Command-line utilities that manipulate BAM files with a Java API.
http://picard.sourceforge.net/
"""
version = "1.68"
url = "http://downloads.sourceforge.net/project/picard/" "picard-tools/%s/picard-tools-%s.zip" % (version, version)
_java_install("picard", version, url, env)
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_gatk_protected(env):
"""Installation script for recent versions of GATK. Requires manual download from user.
http://www.broadinstitute.org/gatk/
"""
min_version = "2.7-2"
version = "%s-g6bda569" % min_version
if shared._symlinked_dir_exists("gatk", version, env, "java"):
return
dl_fname = "GenomeAnalysisTK-%s.tar.bz2" % min_version
print "**** Manual intervention needed"
print "Recent GATK versions require manual download from the GATK website"
print "Please retrieve the latest versions from:"
print "http://www.broadinstitute.org/gatk/download"
print "and place %s in your home directory" % dl_fname
userin = raw_input("**** Press <enter> when complete or type 'skip' to avoid the installation: ")
if userin.find("skip") >= 0:
return
with _make_tmp_dir() as work_dir:
work_fname = os.path.join(work_dir, dl_fname)
def manual_gatk_download(env):
try:
fname = env.safe_run_output("ls $HOME/%s" % dl_fname)
except:
raise IOError("Could not find %s in your home directory. Please download and retry" % dl_fname)
env.safe_put(fname, work_fname)
return work_fname
_java_install("gatk", version, work_fname, env, pre_fetch_fn=manual_gatk_download)
def install_gatk(env):
"""GATK: library for writing efficient analysis tools using next-generation sequencing data
http://www.broadinstitute.org/gsa/wiki/index.php/Home_Page
"""
version = "1.6-11-g3b2fab9"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/" "GenomeAnalysisTK-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
def install_gatk_queue(env):
"""Command-line scripting framework for defining multi-stage genomic analysis pipelines.
http://www.broadinstitute.org/gsa/wiki/index.php/GATK-Queue
"""
version = "1.6-11-g3b2fab9"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/" "Queue-%s%s" % (version, ext)
_java_install("gatk_queue", version, url, env)
def install_picard(env):
"""Command-line utilities that manipulate BAM files with a Java API.
http://picard.sourceforge.net/
"""
version = "1.96"
url = "http://downloads.sourceforge.net/project/picard/" \
"picard-tools/%s/picard-tools-%s.zip" % (version, version)
_java_install("picard", version, url, env)
def install_gatk_queue(env):
"""Command-line scripting framework for defining multi-stage genomic analysis pipelines.
http://www.broadinstitute.org/gsa/wiki/index.php/GATK-Queue
"""
version = "2.1-1-g426e8e7"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/"\
"QueueLite-%s%s" % (version, ext)
_java_install("gatk_queue", version, url, env)
def install_alientrimmer(env):
"""
Adapter removal tool
http://www.ncbi.nlm.nih.gov/pubmed/23912058
"""
version = "0.3.2"
url = ("ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/"
"AlienTrimmer_%s.tar.gz" % version)
_java_install("AlienTrimmer", version, url, env)
def install_alientrimmer(env):
"""
Adapter removal tool
http://www.ncbi.nlm.nih.gov/pubmed/23912058
"""
version = "0.3.2"
url = ("ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/"
"AlienTrimmer_%s.tar.gz" % version)
_java_install("AlienTrimmer", version, url, env)
def install_gatk(env):
"""GATK-lite: library for writing efficient analysis tools using next-generation sequencing data
http://www.broadinstitute.org/gatk/
"""
version = "2.1-1-g426e8e7"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTKLite-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
def install_gatk(env):
"""GATK-lite: library for writing efficient analysis tools using next-generation sequencing data
http://www.broadinstitute.org/gatk/
"""
version = "2.1-1-g426e8e7"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTKLite-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
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)
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)
def install_bio4j(env):
"""Bio4j graph based database: http://www.bio4j.com/
"""
version = "0.7"
url = "https://s3-eu-west-1.amazonaws.com/bio4j-public/releases/" \
"{v}/bio4j-{v}.zip".format(v=version)
def _install_fn(env, install_dir):
targets = ["conf", "doc", "jars", "lib", "README"]
for x in targets:
env.safe_sudo("mv {0} {1}".format(x, install_dir))
_java_install("bio4j", version, url, env, install_fn=_install_fn)
def install_bio4j(env):
"""Bio4j graph based database: http://www.bio4j.com/
"""
version = "0.7"
url = "https://s3-eu-west-1.amazonaws.com/bio4j-public/releases/" \
"{v}/bio4j-{v}.zip".format(v=version)
def _install_fn(env, install_dir):
targets = ["conf", "doc", "jars", "lib", "README"]
for x in targets:
env.safe_sudo("mv {0} {1}".format(x, install_dir))
_java_install("bio4j", version, url, env, install_fn=_install_fn)
def install_tint_proteomics_scripts(env):
default_version = "1.19.19"
version = env.get("tool_version", default_version)
url = "http://artifactory.msi.umn.edu/simple/ext-release-local/msi/umn/edu/tint-proteomics-scripts/%s/tint-proteomics-scripts-%s.zip" % (version, version)
def install_fn(env, install_dir):
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = _get_bin_dir(env)
for script in ["ITraqScanSummarizer", "LTQ-iQuant", "LTQ-iQuant-cli", "MgfFormatter"]:
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, script), bin_dir))
env.safe_sudo("chmod +x '%s'/*" % bin_dir)
_java_install("tint-proteomics-scripts", version, url, env, install_fn)
def install_mzmine(env):
default_version = "2.9.1"
version = env.get("tool_version", default_version)
point_version = version.rsplit('.', 1)[0]
url = "http://downloads.sourceforge.net/project/mzmine/mzmine2/%s/MZmine-%s.zip" % (point_version, version)
def install_fn(env, install_dir):
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = os.path.join(env.get("system_install"), "bin")
env.safe_sudo("mkdir -p '%s'" % bin_dir)
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "startMZmine_Linux.sh"), os.path.join(bin_dir, "MZmine")))
_java_install("mzmine2", version, url, env, install_fn)
def install_peptide_shaker(env):
default_version = "0.19.0"
version = env.get("tool_version", default_version)
url = "http://peptide-shaker.googlecode.com/files/PeptideShaker-%s.zip" % version
def install_fn(env, install_dir):
_get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/ed9b48a0f01cb975f8a9e6e126965c955bbee848/PeptideShaker")
_get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/8a17d5fb589984365284e55a98a455c2b47da54f/PeptideShakerCLI")
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = os.path.join(env.get("system_install"), "bin")
env.safe_sudo("mkdir -p '%s'" % bin_dir)
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShaker"), os.path.join(bin_dir, "PeptideShaker")))
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShakerCLI"), os.path.join(bin_dir, "PeptideShakerCLI")))
_java_install("PeptideShaker", version, url, env, install_fn)
def install_pgdspider(env):
"""PGDSpider format conversion for population genetics programs.
"""
version = "2.0.1.2"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
v=version)
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = os.path.join(env.system_install, "bin")
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
_java_install("PGDSpider", version, url, env, install_fn=_install_fn)
def install_mzmine(env):
default_version = "2.10"
version = env.get("tool_version", default_version)
url = "http://downloads.sourceforge.net/project/mzmine/mzmine2/%s/MZmine-%s.zip" % (version, version)
def install_fn(env, install_dir):
## Enhanced MZmine startup script that works when used a symbolic link and tailored for CloudBioLinux.
_get_gist_script(env, "https://gist.github.com/jmchilton/5474421/raw/15f3b817fa82d5f5e2143ee08bd248efee951d6a/MZmine")
# Hack for multi-user environment.
env.safe_sudo("chmod -R o+w conf")
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = os.path.join(env.get("system_install"), "bin")
env.safe_sudo("mkdir -p '%s'" % bin_dir)
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "MZmine"), os.path.join(bin_dir, "MZmine")))
_java_install("mzmine2", version, url, env, install_fn)
def install_pgdspider(env):
"""PGDSpider format conversion for population genetics programs.
"""
version = "2.0.1.2"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
v=version)
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = os.path.join(env.system_install, "bin")
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
_java_install("PGDSpider", version, url, env, install_fn=_install_fn)
def install_peptide_shaker(env):
default_version = "0.20.0"
version = env.get("tool_version", default_version)
url = "http://peptide-shaker.googlecode.com/files/PeptideShaker-%s.zip" % version
def install_fn(env, install_dir):
_get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/f1fe76d6e6eed99a768ed0b9f41c2d0a6a4b24b7/PeptideShaker")
_get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/8a17d5fb589984365284e55a98a455c2b47da54f/PeptideShakerCLI")
# Hack for multi-user environment.
env.safe_sudo("chmod -R o+w resources")
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = os.path.join(env.get("system_install"), "bin")
env.safe_sudo("mkdir -p '%s'" % bin_dir)
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShaker"), os.path.join(bin_dir, "PeptideShaker")))
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShakerCLI"), os.path.join(bin_dir, "PeptideShakerCLI")))
_java_install("PeptideShaker", version, url, env, install_fn)
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
with quiet():
have_gsalib = run("Rscript -e '\"gsalib\" %in% installed.packages()'")
if have_gsalib and "FALSE" in have_gsalib:
git_repo = "git clone --depth 1 git://github.com/broadgsa/gatk.git"
def install_gsalib(env):
env.safe_sudo("ant gsalib")
_get_install(git_repo, env, install_gsalib)
def install_pgdspider(env):
"""PGDSpider format conversion for population genetics programs.
http://www.cmpg.unibe.ch/software/PGDSpider/
"""
if os.path.exists(os.path.join(shared._get_bin_dir(env), "PGDSpider2.sh")):
return
version = "2.0.2.0"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
v=version)
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = shared._get_bin_dir(env)
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
env.safe_run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
_java_install("PGDSpider", version, url, env, install_fn=_install_fn)
def install_tint_proteomics_scripts(env):
default_version = "1.19.19"
version = env.get("tool_version", default_version)
url = "http://artifactory.msi.umn.edu/simple/ext-release-local/msi/umn/edu/tint-proteomics-scripts/%s/tint-proteomics-scripts-%s.zip" % (
version, version)
def install_fn(env, install_dir):
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = _get_bin_dir(env)
for script in [
"ITraqScanSummarizer", "LTQ-iQuant", "LTQ-iQuant-cli",
"MgfFormatter"
]:
env.safe_sudo("ln -s '%s' %s" %
(os.path.join(install_dir, script), bin_dir))
env.safe_sudo("chmod +x '%s'/*" % bin_dir)
_java_install("tint-proteomics-scripts", version, url, env, install_fn)
def install_pgdspider(env):
"""PGDSpider format conversion for population genetics programs.
http://www.cmpg.unibe.ch/software/PGDSpider/
"""
if os.path.exists(os.path.join(shared._get_bin_dir(env), "PGDSpider2.sh")):
return
version = "2.0.2.0"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
v=version)
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = shared._get_bin_dir(env)
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir,
jar=jar))
env.safe_run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
_java_install("PGDSpider", version, url, env, install_fn=_install_fn)
def install_mzmine(env):
default_version = "2.10"
version = env.get("tool_version", default_version)
url = "http://downloads.sourceforge.net/project/mzmine/mzmine2/%s/MZmine-%s.zip" % (
version, version)
def install_fn(env, install_dir):
## Enhanced MZmine startup script that works when used a symbolic link and tailored for CloudBioLinux.
_get_gist_script(
env,
"https://gist.github.com/jmchilton/5474421/raw/15f3b817fa82d5f5e2143ee08bd248efee951d6a/MZmine"
)
# Hack for multi-user environment.
env.safe_sudo("chmod -R o+w conf")
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = os.path.join(env.get("system_install"), "bin")
env.safe_sudo("mkdir -p '%s'" % bin_dir)
env.safe_sudo("ln -s '%s' %s" % (os.path.join(
install_dir, "MZmine"), os.path.join(bin_dir, "MZmine")))
_java_install("mzmine2", version, url, env, install_fn)
def install_gatk_protected(env):
"""Installation script for recent versions of GATK. Requires manual download from user.
http://www.broadinstitute.org/gatk/
"""
min_version = "2.6-5"
version = "%s-gba531bd" % min_version
dl_fname = "GenomeAnalysisTK-%s.tar.bz2" % min_version
with _make_tmp_dir() as work_dir:
work_fname = os.path.join(work_dir, dl_fname)
def manual_gatk_download(env):
print "**** Manual intervention needed"
print "Recent GATK versions require manual download from the GATK website"
print "Please retrieve the latest versions from:"
print "http://www.broadinstitute.org/gatk/download"
print "and place %s in your home directory" % dl_fname
raw_input("**** Press <enter> when complete ")
try:
fname = env.safe_run_output("ls $HOME/%s" % dl_fname)
except:
raise IOError("Could not find %s in your home directory. Please download and retry" % dl_fname)
env.safe_put(fname, work_fname)
return work_fname
_java_install("gatk", version, work_fname, env, pre_fetch_fn=manual_gatk_download)
def install_gatk(env):
version = "1.4-8-g63b7a70"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/" "GenomeAnalysisTK-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
def install_picard(env):
version = "1.52"
url = "http://downloads.sourceforge.net/project/picard/" \
"picard-tools/%s/picard-tools-%s.zip" % (version, version)
_java_install("picard", version, url, env)
def install_gatk(env):
version = "1.1-35-ge253f6f"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTK-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
def install_gatk_queue(env):
version = "1.0.4052"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/"\
"Queue-%s%s" % (version, ext)
_java_install("gatk_queue", version, url, env)
def install_picard(env):
version = "1.60"
url = "http://downloads.sourceforge.net/project/picard/" "picard-tools/%s/picard-tools-%s.zip" % (version, version)
_java_install("picard", version, url, env)
def install_gatk_queue(env):
version = "1.4-8-g63b7a70"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/" "Queue-%s%s" % (version, ext)
_java_install("gatk_queue", version, url, env)