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(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)