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):
out_file = shared._remote_fetch(env, url)
env.safe_run("tar -xzvpf %s" % out_file)
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_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))
