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): """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 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 = "1.1.5" 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_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_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_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_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_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 = $RealBin;") env.safe_sudo("chmod a+rwx %s" % x) env.safe_sudo("mv * %s" % install_dir) for x in executables: env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, x, env.system_install, x))
def install_tassel(env): """TASSEL: evaluate traits associations, evolutionary patterns, and linkage disequilibrium. http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&/Itemid=119 """ version = "5" build_id = "1140d3fceb75" url = "https://bitbucket.org/tasseladmin/tassel-{0}-standalone/get/{1}.zip".format(version, build_id) executables = ["start_tassel.pl", "run_pipeline.pl"] install_dir = _symlinked_java_version_dir("tassel", version, env) if install_dir: with _make_tmp_dir() as work_dir: with cd(work_dir): dl_file = shared._remote_fetch(env, url) env.safe_run("unzip %s" % dl_file) with cd("tasseladmin-tassel-{0}-standalone-{1}".format(version, build_id)): for x in executables: env.safe_sed(x, "^my \$top.*;", "use FindBin qw($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))