def install_novoalign(env):
base_version = "V2.07.09"
cs_version = "V1.01.09"
_url = "http://www.novocraft.com/downloads/%s/" % base_version
ref_url = "http://www.novocraft.com/main/downloadpage.php"
base_url = "%s/novocraft%s.gcc.tar.gz" % (_url, base_version)
cs_url = "%s/novoalignCS%s.gcc.tar.gz" % (_url, cs_version)
install_dir = os.path.join(env.system_install, "bin")
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, base_url)
run("tar -xzvpf novocraft%s.gcc.tar.gz" % base_version)
with cd("novocraft"):
for fname in ["isnovoindex", "novo2maq", "novo2paf",
"novo2sam.pl", "novoalign", "novobarcode",
"novoindex", "novope2bed.pl", "novorun.pl",
"novoutil"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, cs_url)
run("tar -xzvpf novoalignCS%s.gcc.tar.gz" % cs_version)
with cd("novoalignCS"):
for fname in ["novoalignCS"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def install_novoalign(env):
"""Novoalign short read aligner using Needleman-Wunsch algorithm with affine gap penalties.
http://www.novocraft.com/main/index.php
"""
base_version = "V3.00.02"
cs_version = "V1.03.02"
_url = "http://www.novocraft.com/downloads/%s/" % base_version
ref_url = "http://www.novocraft.com/main/downloadpage.php"
base_url = "%s/novocraft%s.gcc.tar.gz" % (_url, base_version)
cs_url = "%s/novoalignCS%s.gcc.tar.gz" % (_url, cs_version)
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, base_url)
env.safe_run("tar -xzvpf novocraft%s.gcc.tar.gz" % base_version)
with cd("novocraft"):
for fname in ["isnovoindex", "novo2maq", "novo2paf",
"novo2sam.pl", "novoalign", "novobarcode",
"novoindex", "novope2bed.pl", "novorun.pl",
"novoutil"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, cs_url)
env.safe_run("tar -xzvpf novoalignCS%s.gcc.tar.gz" % cs_version)
with cd("novoalignCS"):
for fname in ["novoalignCS"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def install_anaconda(env):
"""Pre-packaged Anaconda Python installed from Continuum.
http://docs.continuum.io/anaconda/index.html
"""
version = "2.0.0"
outdir = os.path.join(env.system_install, "anaconda")
if env.distribution in ["ubuntu", "centos", "scientificlinux", "debian", "arch", "suse"]:
platform = "Linux"
elif env.distribution in ["macosx"]:
platform = "MacOSX"
else:
raise ValueError("Unexpected distribution: %s" % env.distribution)
url = "http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/" \
"Anaconda-%s-%s-x86_64.sh" % (version, platform)
if not env.safe_exists(outdir):
with _make_tmp_dir() as work_dir:
with cd(work_dir):
installer = shared._remote_fetch(env, url)
env.safe_sed(os.path.basename(url), "more <<EOF", "cat <<EOF")
env.safe_sudo("echo -e '\nyes\n%s\nyes\n' | bash %s" % (outdir, installer))
env.safe_sudo("chown -R %s %s" % (env.user, outdir))
comment_line = "# added by Ananconda %s installer" % version
if not env.safe_contains(env.shell_config, comment_line):
env.safe_append(env.shell_config, comment_line)
env.safe_append(env.shell_config, "export PATH=%s/bin:$PATH" % outdir)
# remove curl library with broken certificates
env.safe_run("%s/bin/conda remove --yes curl" % outdir)
env.safe_run("%s/bin/conda install --yes pip" % outdir)
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_pydoop(env):
"""Install pydoop; provides Hadoop access for Python.
http://pydoop.sourceforge.net/docs/installation.html
"""
hadoop_version = "0.20.2"
pydoop_version = "0.3.7_rc1"
ubuntu_hadoop_src = "/usr/src/hadoop-0.20"
hadoop_url = "http://apache.mirrors.hoobly.com/hadoop/core/" \
"hadoop-%s/hadoop-%s.tar.gz" % (hadoop_version, hadoop_version)
pydoop_url ="http://downloads.sourceforge.net/project/pydoop/" \
"Pydoop-%s/pydoop-%s.tar.gz" % (pydoop_version, pydoop_version)
java_home = env.java_home if env.has_key("java_home") else os.environ["JAVA_HOME"]
pyext = env.python_version_ext if env.has_key("python_version_ext") else ""
with _make_tmp_dir() as work_dir:
with cd(work_dir):
pydoop_dir = _fetch_and_unpack(pydoop_url)
# Use native supplied Hadoop source to match installed defaults. On
# Ubuntu this is currently 0.20.2.
if exists(ubuntu_hadoop_src):
hadoop_dir = ubuntu_hadoop_src
with cd(pydoop_dir):
sed("setup.py", "src/c", "c")
else:
hadoop_dir = _fetch_and_unpack(hadoop_url)
with cd(pydoop_dir):
export_str = "export HADOOP_VERSION=%s && export HADOOP_HOME=%s " \
"&& export JAVA_HOME=%s" % (hadoop_version,
os.path.join(os.pardir, hadoop_dir), java_home)
run("%s && python%s setup.py build" % (export_str, pyext))
sudo("%s && python%s setup.py install --skip-build" %
(export_str, pyext))
def install_snpeff(env):
"""Variant annotation and effect prediction tool.
http://snpeff.sourceforge.net/
"""
version = "3_3"
genomes = ["GRCh37.71", "hg19", "GRCm38.71"]
#genomes_notinstalled = ["NCBIM37.66","athalianaTair10"]
url = "http://downloads.sourceforge.net/project/snpeff/" \
"snpEff_v%s_core.zip" % version
genome_url_base = "http://downloads.sourceforge.net/project/snpeff/"\
"databases/v%s/snpEff_v%s_%s.zip"
install_dir = _symlinked_java_version_dir("snpeff", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
dir_name = _fetch_and_unpack(url)
with cd(dir_name):
env.safe_sudo("mv *.jar %s" % install_dir)
env.safe_run("sed -i.bak -r -e 's/^data_dir.*=.*/data_dir = %s\/data/' %s" %
(install_dir.replace("/", "\/"), "snpEff.config"))
env.safe_run("chmod a+r *.config")
env.safe_sudo("mv *.config %s" % install_dir)
data_dir = os.path.join(install_dir, "data")
env.safe_sudo("mkdir %s" % data_dir)
for org in genomes:
if not env.safe_exists(os.path.join(data_dir, org)):
gurl = genome_url_base % (version, version, org)
_fetch_and_unpack(gurl, need_dir=False)
env.safe_sudo("mv data/%s %s" % (org, data_dir))
def install_snpeff(env):
version = "1_9_5"
genomes = ["hg37.61", "mm37.61"]
url = "http://downloads.sourceforge.net/project/snpeff/" \
"snpEff_v%s_core.zip" % version
genome_url_base = "http://downloads.sourceforge.net/project/snpeff/"\
"databases/v%s/snpEff_v%s_%s.zip"
install_dir = _symlinked_java_version_dir("snpeff", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
dir_name = _fetch_and_unpack(url)
with cd(dir_name):
env.safe_sudo("mv *.jar %s" % install_dir)
run("sed -i.bak -r -e 's/data_dir = \.\/data\//data_dir = %s\/data/' %s" %
(install_dir.replace("/", "\/"), "snpEff.config"))
run("chmod a+r *.config")
env.safe_sudo("mv *.config %s" % install_dir)
data_dir = os.path.join(install_dir, "data")
env.safe_sudo("mkdir %s" % data_dir)
for org in genomes:
if not exists(os.path.join(data_dir, org)):
gurl = genome_url_base % (version, version, org)
_fetch_and_unpack(gurl, need_dir=False)
env.safe_sudo("mv data/%s %s" % (org, data_dir))
def _unzip_install(pname, version, url, env, install_fn, dir_name="."):
install_dir = _symlinked_java_version_dir(pname, version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
with cd(dir_name):
install_fn(env, install_dir)
def install_solexaqa(env):
version = "1.4"
url = "http://downloads.sourceforge.net/project/solexaqa/src/" "SolexaQA_v.%s.pl.zip" % version
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
run("unzip %s" % os.path.basename(url))
env.safe_sudo("mv SolexaQA.pl %s" % os.path.join(env.system_install, "bin"))
def _download_executables(env, base_url, tools):
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
for tool in tools:
final_tool = os.path.join(install_dir, tool)
if not env.safe_exists(final_tool) and shared._executable_not_on_path(tool):
shared._remote_fetch(env, "%s%s" % (base_url, tool))
env.safe_sudo("cp -f %s %s" % (tool, install_dir))
def _install_tar_ball(env, url, tool):
install_dir = shared._get_bin_dir(env)
install_dir_parent = os.path.abspath(os.path.join(install_dir, os.pardir))
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_remote_fetch(env, url + tool + ".tar.gz")
env.safe_sudo("tar -xzvpf %s.tar.gz -C %s" % (tool, install_dir_parent))
env.safe_sudo("chown -R %s:%s '%s'" % (env.user, env.user, install_dir))
env.safe_sudo("chgrp -R %s '%s'" % (env.user, install_dir))
def install_leinengin(env):
"""Standard clojure build tool: http://github.com/technomancy/leiningen
"""
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget --no-check-certificate https://github.com/technomancy/leiningen/raw/stable/bin/lein")
run("chmod a+rwx lein")
env.safe_sudo("mv lein %s" % os.path.join(env.system_install, "bin"))
run("lein self-install")
def install_leinengin(env):
"""Clojure tool for project configuration and automation.
http://github.com/technomancy/leiningen
"""
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget --no-check-certificate https://raw.github.com/technomancy/leiningen/preview/bin/lein")
run("chmod a+rwx lein")
env.safe_sudo("mv lein %s" % os.path.join(env.system_install, "bin"))
run("lein self-install")
def install_bx_python(env):
"""Install bx-python
"""
clone_url = "http://bitbucket.org/james_taylor/bx-python"
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("hg clone %s" % clone_url)
with cd(os.path.split(clone_url)[-1]):
run("python setup.py build")
sudo("python setup.py install --skip-build")
def install_leiningen(env):
"""Clojure tool for project configuration and automation.
http://github.com/technomancy/leiningen
"""
bin_dir = os.path.join(env.system_install, "bin")
with _make_tmp_dir() as work_dir:
with cd(work_dir):
shared._remote_fetch(env, "https://raw.github.com/technomancy/leiningen/stable/bin/lein")
env.safe_run("chmod a+rwx lein")
env.safe_sudo("mv lein %s" % bin_dir)
env.safe_run("%s/lein" % bin_dir)
def install_proteowizard(env):
url = "http://teamcity.labkey.org:8080/repository/download/bt36/77483:id/pwiz-bin-windows-x86-vc100-release-3_0_4360.tar.bz2?guest=1"
install_dir = env.get("install_dir")
share_dir = "%s/share/proteowizard" % install_dir
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
env.safe_sudo("cp -r . '%s'" % share_dir)
proteowizard_apps = ["msconvert", "msaccess", "chainsaw", "msdiff", "mspicture", "mscat", "txt2mzml", "MSConvertGUI", "Skyline", "Topograph", "SeeMS"]
for app in proteowizard_apps:
setup_wine_wrapper(env, "%s/%s" % (share_dir, app))
def install_sambamba(env):
"""Library for working with SAM/BAM formats written in D programming language
https://github.com/lomereiter/sambamba/wiki
"""
version = "0.2.9"
url = "https://github.com/downloads/lomereiter/sambamba/" "sambamba-{0}_amd64.deb".format(version)
if env.distribution in ["ubuntu", "debian"] and env.is_64bit:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget {0}".format(url))
env.safe_sudo("sudo dpkg -i {0}".format(os.path.basename(url)))
def install_mutect(env):
version = "1.1.5"
url = "https://github.com/broadinstitute/mutect/releases/download/" \
"%s/muTect-%s-bin.zip" % (version, version)
install_dir = _symlinked_java_version_dir("mutect", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget --no-check-certificate %s" % url)
env.safe_run("unzip %s" % os.path.basename(url))
env.safe_sudo("mv *.jar version.txt LICENSE* %s" % install_dir)
def install_mutect(env):
version = "1.1.5"
url = "https://github.com/broadinstitute/mutect/releases/download/" \
"%s/muTect-%s-bin.zip" % (version, version)
install_dir = _symlinked_java_version_dir("mutect", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
out_file = shared._remote_fetch(env, url)
env.safe_run("unzip %s" % out_file)
env.safe_sudo("mv *.jar version.txt LICENSE* %s" % install_dir)
def install_solexaqa(env):
"""SolexaQA creates visual representations of data quality from FASTQ files.
http://solexaqa.sourceforge.net/
"""
version = "1.4"
url = "http://downloads.sourceforge.net/project/solexaqa/src/" "SolexaQA_v.%s.pl.zip" % version
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
run("unzip %s" % os.path.basename(url))
env.safe_sudo("mv SolexaQA.pl %s" % os.path.join(env.system_install, "bin"))
def install_mutect(env):
version = "1.1.4"
url = "http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/" \
"muTect-%s-bin.zip" % version
install_dir = _symlinked_java_version_dir("mutect", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget --no-check-certificate %s" % url)
env.safe_run("unzip %s" % os.path.basename(url))
env.safe_sudo("mv *.jar version.txt LICENSE* %s" % install_dir)
def install_morpheus(env):
url = "http://www.chem.wisc.edu/~coon/Downloads/Morpheus/latest/Morpheus.zip" # TODO:
install_dir = env.get("install_dir")
share_dir = "%s/share/morpheus" % install_dir
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
env.safe_sudo("cp -r Morpheus '%s'" % share_dir)
morpheus_exes = ["morpheus_cl.exe", "Morpheus.exe"]
for app in morpheus_exes:
setup_wine_wrapper(env, "%s/%s" % (share_dir, app))
def install_pysam(env):
"""Install pysam for Python access to BAM files.
"""
version = "0.3"
url = "http://pysam.googlecode.com/files/pysam-%s.tar.gz" % version
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
run("tar -xzvpf %s" % os.path.split(url)[-1])
with cd("pysam-%s" % version):
run("python setup.py build")
sudo("python setup.py install --skip-build")
def install_bx_python(env):
"""Install bx-python
"""
clone_url = "http://bitbucket.org/james_taylor/bx-python"
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("hg clone %s" % clone_url)
with cd(os.path.split(clone_url)[-1]):
run("python%s setup.py build" % env.python_version_ext)
sudo("python%s setup.py install --skip-build" % env.python_version_ext)
sudo("rm -rf dist")
sudo("rm -rf lib/bx_python.egg-info")
def install_picard(env):
version = "1.49"
url = "http://downloads.sourceforge.net/project/picard/" \
"picard-tools/%s/picard-tools-%s.zip" % (version, version)
install_dir = _symlinked_java_version_dir("picard", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % (url))
run("unzip %s" % os.path.basename(url))
with cd(os.path.splitext(os.path.basename(url))[0]):
env.safe_sudo("mv *.jar %s" % install_dir)
def install_varscan(env):
"""Variant detection in massively parallel sequencing data
http://varscan.sourceforge.net/
"""
version = "2.3.6"
url = "http://downloads.sourceforge.net/project/varscan/VarScan.v%s.jar" % version
install_dir = _symlinked_java_version_dir("varscan", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
out_file = shared._remote_fetch(env, url)
env.safe_sudo("mv %s %s" % (out_file, install_dir))
def install_bcbio_variation(env):
"""Toolkit to analyze genomic variation data with comparison and ensemble approaches.
https://github.com/chapmanb/bcbio.variation
"""
version = "0.0.6"
url = "https://s3.amazonaws.com/bcbio.variation/" "bcbio.variation-%s-standalone.jar" % version
install_dir = _symlinked_java_version_dir("bcbio_variation", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
env.safe_sudo("mv *.jar %s" % install_dir)
def install_ms2preproc(env):
default_version = "2009"
version = env.get("tool_version", default_version)
get_cmd = 'wget --post-data "Anonym=1&GotoDownload=1&ref=http://hci.iwr.uni-heidelberg.de/MIP/Software/ms2preproc.php" http://hci.iwr.uni-heidelberg.de/php-tools/download.php -O ms2preproc.zip'
install_dir = _get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run(get_cmd)
run("unzip ms2preproc.zip")
run("chmod +x ms2preproc-x86_64")
env.safe_sudo("mv ms2preproc-x86_64 '%s'/ms2preproc" % install_dir)
def install_sambamba(env):
"""Library for working with SAM/BAM formats written in D programming language
https://github.com/lomereiter/sambamba/wiki
"""
version = "0.2.9"
url = "https://github.com/downloads/lomereiter/sambamba/" \
"sambamba-{0}_amd64.deb".format(version)
if env.distribution in ["ubuntu", "debian"] and env.is_64bit:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
dl_file = shared._remote_fetch(env, url)
env.safe_sudo("sudo dpkg -i {0}".format(dl_file))
def install_varscan(env):
"""Variant detection in massively parallel sequencing data
http://varscan.sourceforge.net/
"""
version = "2.3.5"
url = "http://downloads.sourceforge.net/project/varscan/VarScan.v%s.jar" % version
install_dir = _symlinked_java_version_dir("varscan", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget --no-check-certificate %s" % url)
env.safe_sudo("mv *.jar %s" % install_dir)
def install_shrec(env):
version = "2.2"
url = "http://downloads.sourceforge.net/project/shrec-ec/SHREC%%20%s/bin.zip" % version
install_dir = _symlinked_java_version_dir("shrec", version, env)
if install_dir:
shrec_script = "%s/shrec" % install_dir
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % (url))
run("unzip %s" % os.path.basename(url))
env.safe_sudo("mv *.class %s" % install_dir)
for line in _shrec_run.split("\n"):
if line.strip():
append(shrec_script, line, use_sudo=env.use_sudo)
env.safe_sudo("chmod a+rwx %s" % shrec_script)
env.safe_sudo("ln -s %s %s/bin/shrec" %
(shrec_script, env.system_install))
def install_proteowizard(env):
build_id = "83083"
version = "3_0_4472"
url = "http://teamcity.labkey.org:8080/repository/download/bt36/%s:id/pwiz-bin-windows-x86-vc100-release-%s.tar.bz2?guest=1" % (
build_id, version)
install_dir = env.get("install_dir")
share_dir = "%s/share/proteowizard" % install_dir
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
env.safe_sudo("cp -r . '%s'" % share_dir)
proteowizard_apps = [
"msconvert", "msaccess", "chainsaw", "msdiff", "mspicture", "mscat",
"txt2mzml", "MSConvertGUI", "Skyline", "Topograph", "SeeMS"
]
for app in proteowizard_apps:
setup_wine_wrapper(env, "%s/%s" % (share_dir, app))
def install_gemini(env):
"""A lightweight db framework for disease and population genetics.
https://github.com/arq5x/gemini
"""
version = "github"
installer = "https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py"
data_dir = os.path.join(
env.system_install,
"local" if env.system_install.find("/local") == -1 else "", "share",
"gemini")
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget --no-check-certificate %s" % installer)
env.safe_run("%s gemini_install.py %s %s %s" %
(_python_cmd(env), "" if env.use_sudo else "--nosudo",
env.system_install, data_dir))
env.safe_run("rm -f gemini_install.py")
def install_novosort(env):
"""Multithreaded sort and merge for BAM files.
http://www.novocraft.com/wiki/tiki-index.php?page=Novosort
"""
base_version = "V3.00.02"
version = "V1.00.02"
url = "http://www.novocraft.com/downloads/%s/novosort%s.gcc.tar.gz" % (
base_version, version)
ref_url = "http://www.novocraft.com/main/downloadpage.php"
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, url)
env.safe_run("tar -xzvpf novosort%s.gcc.tar.gz" % version)
with cd("novosort"):
for fname in ["novosort"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def install_fastqc(env):
version = "0.9.1"
url = "http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/" \
"fastqc_v%s.zip" % version
executable = "fastqc"
install_dir = _symlinked_java_version_dir("fastqc", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % (url))
run("unzip %s" % os.path.basename(url))
with cd("FastQC"):
env.safe_sudo("chmod a+rwx %s" % executable)
env.safe_sudo("mv * %s" % install_dir)
env.safe_sudo(
"ln -s %s/%s %s/bin/%s" %
(install_dir, executable, env.system_install, executable))
def install_fastq_screen(env):
"""A screening application for high througput sequence data.
http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
"""
version = "0.4"
url = "http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" \
"fastq_screen_v%s.tar.gz" % version
install_dir = shared._symlinked_shared_dir("fastqc_screen", version, env)
executable = "fastq_screen"
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % (url))
env.safe_run("tar -xzvpf %s" % os.path.basename(url))
with cd("fastq_screen_v%s" % version):
env.safe_sudo("mv * %s" % install_dir)
env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, executable,
env.system_install, executable))
def install_multiplierz(env):
"""
Assumes your wine environment contains an install Python 2.6
in C:\Python26.
"""
wine_user = _get_wine_user(env)
env.safe_sudo("setup_proteomics_wine_env.sh", user=wine_user)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(
"hg clone http://multiplierz.hg.sourceforge.net:8000/hgroot/multiplierz/multiplierz"
)
with cd("multiplierz"):
wine_prefix = _get_wine_prefix(env)
env.safe_sudo(
"%s; wine %s/drive_c/Python26/python.exe setup.py install"
% (_conf_wine(env), wine_prefix),
user=wine_user)
def install_fastqc(env):
"""A quality control tool for high throughput sequence data.
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
"""
version = "0.10.1"
url = "http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/" \
"fastqc_v%s.zip" % version
executable = "fastqc"
install_dir = _symlinked_java_version_dir("fastqc", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % (url))
env.safe_run("unzip %s" % os.path.basename(url))
with cd("FastQC"):
env.safe_sudo("chmod a+rwx %s" % executable)
env.safe_sudo("mv * %s" % install_dir)
env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, executable,
env.system_install, executable))
def install_tassel(env):
"""TASSEL: evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&/Itemid=119
"""
version = "4.0"
url = "http://www.maizegenetics.net/tassel/tassel{0}_standalone.zip".format(version)
executables = ["start_tassel.pl", "run_pipeline.pl"]
install_dir = _symlinked_java_version_dir("tassel", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % (url))
env.safe_run("unzip %s" % os.path.basename(url))
with cd("tassel{0}_standalone".format(version)):
for x in executables:
env.safe_sed(x, "^my \$top.*;",
"use FindBin qw($RealBin); my $top = $RealBin;")
env.safe_sudo("chmod a+rwx %s" % x)
env.safe_sudo("mv * %s" % install_dir)
for x in executables:
env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, x,
env.system_install, x))
def install_shrec(env):
"""Shrec is a bioinformatics tool for error correction of HTS read data.
http://sourceforge.net/projects/shrec-ec/
"""
version = "2.2"
url = "http://downloads.sourceforge.net/project/shrec-ec/SHREC%%20%s/bin.zip" % version
install_dir = _symlinked_java_version_dir("shrec", version, env)
if install_dir:
shrec_script = "%s/shrec" % install_dir
with _make_tmp_dir() as work_dir:
with cd(work_dir):
out_file = shared._remote_fetch(env, url)
env.safe_run("unzip %s" % out_file)
env.safe_sudo("mv *.class %s" % install_dir)
for line in _shrec_run.split("\n"):
if line.strip():
env.safe_append(shrec_script,
line,
use_sudo=env.use_sudo)
env.safe_sudo("chmod a+rwx %s" % shrec_script)
env.safe_sudo("ln -s %s %s/bin/shrec" %
(shrec_script, env.system_install))
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_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_snpeff(env):
version = "1_9"
genomes = ["hg37.61", "mm37.61"]
url = "http://downloads.sourceforge.net/project/snpeff/" \
"snpEff_v%s_core.zip" % version
genome_url_base = "http://downloads.sourceforge.net/project/snpeff/"\
"databases/v%s/snpEff_v%s_%s.zip"
install_dir = _symlinked_java_version_dir("snpeff", version)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
dir_name = _fetch_and_unpack(url)
with cd(dir_name):
sudo("mv *.jar %s" % install_dir)
run("sed -i.bak -r -e 's/data_dir = \.\/data\//data_dir = %s\/data/' %s"
% (install_dir.replace("/", "\/"), "snpEff.config"))
sudo("mv *.config %s" % install_dir)
data_dir = os.path.join(install_dir, "data")
sudo("mkdir %s" % data_dir)
for org in genomes:
if not exists(os.path.join(data_dir, org)):
gurl = genome_url_base % (version, version, org)
_fetch_and_unpack(gurl, need_dir=False)
sudo("mv data/%s %s" % (org, data_dir))
