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 = "5"
build_id = "1140d3fceb75"
url = "https://bitbucket.org/tasseladmin/tassel-{0}-standalone/get/{1}.zip".format(
version, build_id)
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):
dl_file = shared._remote_fetch(env, url)
env.safe_run("unzip %s" % dl_file)
with cd("tasseladmin-tassel-{0}-standalone-{1}".format(
version, build_id)):
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_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 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 install_snpeff(env):
"""Variant annotation and effect prediction tool.
http://snpeff.sourceforge.net/
"""
version = "3_4"
genomes = []
#genomes = ["GRCh37.74", "hg19", "GRCm38.74", "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 -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 _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 _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_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_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_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_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_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_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_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_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 = "2.3.5"
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_bcbio_variation(env):
"""Toolkit to analyze genomic variation data with comparison and ensemble approaches.
https://github.com/chapmanb/bcbio.variation
"""
version = "0.1.6"
url = "https://github.com/chapmanb/bcbio.variation/releases/download/" \
"v%s/bcbio.variation-%s-standalone.jar" % (version, 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):
jar_file = shared._remote_fetch(env, url)
env.safe_sudo("mv %s %s" % (jar_file, install_dir))
def install_rnaseqc(env):
"""Quality control metrics for RNA-seq data
https://www.broadinstitute.org/cancer/cga/rna-seqc
"""
version = "1.1.7"
url = ("http://www.broadinstitute.org/cancer/cga/sites/default/files/"
"data/tools/rnaseqc/RNA-SeQC_v%s.jar" % version)
install_dir = _symlinked_java_version_dir("RNA-SeQC", 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_sudo("mv *.jar %s" % install_dir)
def install_cram(env):
"""Highly efficient and tunable reference-based compression of sequence data.
http://www.ebi.ac.uk/ena/about/cram_toolkit/
"""
version = "2.0"
url = "https://github.com/vadimzalunin/crammer/raw/master/" \
"cramtools-%s.jar" % version
install_dir = _symlinked_java_version_dir("cram", 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_rnaseqc(env):
"""Quality control metrics for RNA-seq data
https://www.broadinstitute.org/cancer/cga/rna-seqc
"""
version = "1.1.7"
url = ("http://www.broadinstitute.org/cancer/cga/sites/default/files/"
"data/tools/rnaseqc/RNA-SeQC_v%s.jar" % version)
install_dir = _symlinked_java_version_dir("RNA-SeQC", 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_rnaseqc(env):
"""Quality control metrics for RNA-seq data
https://www.broadinstitute.org/cancer/cga/rna-seqc
"""
version = "1.1.7"
url = ("https://github.com/chapmanb/RNA-SeQC/releases/download/"
"v%s/RNA-SeQC_v%s.jar" % (version, version))
install_dir = _symlinked_java_version_dir("RNA-SeQC", 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_cram(env):
"""Highly efficient and tunable reference-based compression of sequence data.
http://www.ebi.ac.uk/ena/about/cram_toolkit/
"""
version = "2.0"
url = "https://github.com/vadimzalunin/crammer/raw/master/" \
"cramtools-%s.jar" % version
install_dir = _symlinked_java_version_dir("cram", 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_bcbio_variation(env):
"""Toolkit to analyze genomic variation data with comparison and ensemble approaches.
https://github.com/chapmanb/bcbio.variation
"""
version = "0.0.9"
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_gatk(env):
version = "1.1"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTK-%s%s" % (version, ext)
install_dir = _symlinked_java_version_dir("gatk", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % (url))
run("tar -xjvpf %s" % os.path.basename(url))
with cd(os.path.basename(url).replace(ext, "")):
env.safe_sudo("mv *.jar %s" % install_dir)
def install_gatk(env):
version = "1.1"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTK-%s%s" % (version, ext)
install_dir = _symlinked_java_version_dir("gatk", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % (url))
run("tar -xjvpf %s" % os.path.basename(url))
with cd(os.path.basename(url).replace(ext, "")):
env.safe_sudo("mv *.jar %s" % 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 = "0.1.0"
url = "https://github.com/chapmanb/bcbio.variation/releases/download/" \
"v%s/bcbio.variation-%s-standalone.jar" % (version, 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):
jar_file = shared._remote_fetch(env, url)
env.safe_sudo("mv %s %s" % (jar_file, install_dir))
def install_rnaseqc(env):
"""Quality control metrics for RNA-seq data
https://www.broadinstitute.org/cancer/cga/rna-seqc
"""
version = "1.1.7"
url = ("http://www.broadinstitute.org/cancer/cga/sites/default/files/"
"data/tools/rnaseqc/RNA-SeQC_v%s.jar" % version)
install_dir = _symlinked_java_version_dir("RNA-SeQC", 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_cram(env):
"""Highly efficient and tunable reference-based compression of sequence data.
http://www.ebi.ac.uk/ena/about/cram_toolkit/
"""
version = "2.0"
url = "https://github.com/vadimzalunin/crammer/raw/master/" \
"cramtools-%s.jar" % version
install_dir = _symlinked_java_version_dir("cram", 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_rnaseqc(env):
"""Quality control metrics for RNA-seq data
https://www.broadinstitute.org/cancer/cga/rna-seqc
"""
version = "1.1.7"
url = ("https://github.com/chapmanb/RNA-SeQC/releases/download/"
"v%s/RNA-SeQC_v%s.jar" % (version, version))
install_dir = _symlinked_java_version_dir("RNA-SeQC", 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_cram(env):
"""Highly efficient and tunable reference-based compression of sequence data.
http://www.ebi.ac.uk/ena/about/cram_toolkit/
"""
version = "2.0"
url = "https://github.com/vadimzalunin/crammer/raw/master/" \
"cramtools-%s.jar" % version
install_dir = _symlinked_java_version_dir("cram", 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_fastqc(env):
version = "0.10.0"
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_fastqc(env):
version = "0.10.0"
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_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_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_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_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_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):
out_file = shared._remote_fetch(env, url)
env.safe_run("unzip %s" % out_file)
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 = "3.0"
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):
run("wget %s" % (url))
run("unzip %s" % os.path.basename(url))
with cd("tassel{0}_standalone".format(version)):
for x in executables:
sed(x, "^my \$top.*;", "use FindBin qw($RealBin); my $top = $RealBin;")
env.safe_sudo("chmod a+rwx %s" % x)
env.safe_sudo("mv * %s" % install_dir)
for x in executables:
env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, x, env.system_install, x))
def install_tassel(env):
"""TASSEL: evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&/Itemid=119
"""
version = "4.0"
url = "http://www.maizegenetics.net/tassel/tassel{0}_standalone.zip".format(version)
executables = ["start_tassel.pl", "run_pipeline.pl"]
install_dir = _symlinked_java_version_dir("tassel", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % (url))
env.safe_run("unzip %s" % os.path.basename(url))
with cd("tassel{0}_standalone".format(version)):
for x in executables:
env.safe_sed(x, "^my \$top.*;",
"use FindBin qw($RealBin); my $top = $RealBin;")
env.safe_sudo("chmod a+rwx %s" % x)
env.safe_sudo("mv * %s" % install_dir)
for x in executables:
env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, x,
env.system_install, x))
def install_shrec(env):
"""Shrec is a bioinformatics tool for error correction of HTS read data.
http://sourceforge.net/projects/shrec-ec/
"""
version = "2.2"
url = "http://downloads.sourceforge.net/project/shrec-ec/SHREC%%20%s/bin.zip" % version
install_dir = _symlinked_java_version_dir("shrec", version, env)
if install_dir:
shrec_script = "%s/shrec" % install_dir
with _make_tmp_dir() as work_dir:
with cd(work_dir):
out_file = shared._remote_fetch(env, url)
env.safe_run("unzip %s" % out_file)
env.safe_sudo("mv *.class %s" % install_dir)
for line in _shrec_run.split("\n"):
if line.strip():
env.safe_append(shrec_script,
line,
use_sudo=env.use_sudo)
env.safe_sudo("chmod a+rwx %s" % shrec_script)
env.safe_sudo("ln -s %s %s/bin/shrec" %
(shrec_script, env.system_install))
def install_tassel(env):
"""TASSEL: evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&/Itemid=119
"""
version = "5"
build_id = "1140d3fceb75"
url = "https://bitbucket.org/tasseladmin/tassel-{0}-standalone/get/{1}.zip".format(version, build_id)
executables = ["start_tassel.pl", "run_pipeline.pl"]
install_dir = _symlinked_java_version_dir("tassel", version, env)
if install_dir:
with _make_tmp_dir() as work_dir:
with cd(work_dir):
dl_file = shared._remote_fetch(env, url)
env.safe_run("unzip %s" % dl_file)
with cd("tasseladmin-tassel-{0}-standalone-{1}".format(version, build_id)):
for x in executables:
env.safe_sed(x, "^my \$top.*;",
"use FindBin qw($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))
