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)