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))