def _cmake_bamtools(env):
env.safe_run("mkdir build")
with cd("build"):
env.safe_run("cmake ..")
env.safe_run("make")
env.safe_sudo("cp bin/* %s" % shared._get_bin_dir(env))
env.safe_sudo("cp lib/* %s" % shared._get_lib_dir(env))
def install_novoalign(env):
"""Novoalign short read aligner using Needleman-Wunsch algorithm with affine gap penalties.
http://www.novocraft.com/main/index.php
"""
base_version = "V3.00.02"
cs_version = "V1.03.02"
_url = "http://www.novocraft.com/downloads/%s/" % base_version
ref_url = "http://www.novocraft.com/main/downloadpage.php"
base_url = "%s/novocraft%s.gcc.tar.gz" % (_url, base_version)
cs_url = "%s/novoalignCS%s.gcc.tar.gz" % (_url, cs_version)
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, base_url)
env.safe_run("tar -xzvpf novocraft%s.gcc.tar.gz" % base_version)
with cd("novocraft"):
for fname in [
"isnovoindex", "novo2maq", "novo2paf", "novo2sam.pl",
"novoalign", "novobarcode", "novoindex",
"novope2bed.pl", "novorun.pl", "novoutil"
]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, cs_url)
env.safe_run("tar -xzvpf novoalignCS%s.gcc.tar.gz" % cs_version)
with cd("novoalignCS"):
for fname in ["novoalignCS"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def install_novoalign(env):
"""Novoalign short read aligner using Needleman-Wunsch algorithm with affine gap penalties.
http://www.novocraft.com/main/index.php
"""
base_version = "V3.00.02"
cs_version = "V1.03.02"
_url = "http://www.novocraft.com/downloads/%s/" % base_version
ref_url = "http://www.novocraft.com/main/downloadpage.php"
base_url = "%s/novocraft%s.gcc.tar.gz" % (_url, base_version)
cs_url = "%s/novoalignCS%s.gcc.tar.gz" % (_url, cs_version)
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, base_url)
env.safe_run("tar -xzvpf novocraft%s.gcc.tar.gz" % base_version)
with cd("novocraft"):
for fname in ["isnovoindex", "novo2maq", "novo2paf",
"novo2sam.pl", "novoalign", "novobarcode",
"novoindex", "novope2bed.pl", "novorun.pl",
"novoutil"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, cs_url)
env.safe_run("tar -xzvpf novoalignCS%s.gcc.tar.gz" % cs_version)
with cd("novoalignCS"):
for fname in ["novoalignCS"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def _cmake_bamtools(env):
env.safe_run("mkdir build")
with cd("build"):
env.safe_run("cmake ..")
env.safe_run("make")
env.safe_sudo("cp bin/* %s" % shared._get_bin_dir(env))
env.safe_sudo("cp lib/* %s" % shared._get_lib_dir(env))
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = shared._get_bin_dir(env)
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
env.safe_run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
def _install_tar_ball(env, url, tool):
install_dir = shared._get_bin_dir(env)
install_dir_parent = os.path.abspath(os.path.join(install_dir, os.pardir))
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_remote_fetch(env, url + tool + ".tar.gz")
env.safe_sudo("tar -xzvpf %s.tar.gz -C %s" % (tool, install_dir_parent))
env.safe_sudo("chown -R %s:%s '%s'" % (env.user, env.user, install_dir))
env.safe_sudo("chgrp -R %s '%s'" % (env.user, install_dir))
def _download_executables(env, base_url, tools):
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
for tool in tools:
final_tool = os.path.join(install_dir, tool)
if not env.safe_exists(final_tool) and shared._executable_not_on_path(tool):
env.safe_run("wget %s%s" % (base_url, tool))
env.safe_sudo("cp -f %s %s" % (tool, install_dir))
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = shared._get_bin_dir(env)
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir,
jar=jar))
env.safe_run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
def _download_executables(env, base_url, tools):
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
for tool in tools:
final_tool = os.path.join(install_dir, tool)
if not env.safe_exists(final_tool) and shared._executable_not_on_path(tool):
shared._remote_fetch(env, "%s%s" % (base_url, tool))
env.safe_sudo("cp -f %s %s" % (tool, install_dir))
def install_solexaqa(env):
"""SolexaQA creates visual representations of data quality from FASTQ files.
http://solexaqa.sourceforge.net/
"""
version = "1.4"
url = "http://downloads.sourceforge.net/project/solexaqa/src/" \
"SolexaQA_v.%s.pl.zip" % version
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))
env.safe_sudo("mv SolexaQA.pl %s" % shared._get_bin_dir(env))
def install_solexaqa(env):
"""SolexaQA creates visual representations of data quality from FASTQ files.
http://solexaqa.sourceforge.net/
"""
version = "1.4"
url = "http://downloads.sourceforge.net/project/solexaqa/src/" \
"SolexaQA_v.%s.pl.zip" % version
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))
env.safe_sudo("mv SolexaQA.pl %s" % shared._get_bin_dir(env))
def _safe_ncurses_make(env):
"""Combine samtools, removing ncurses refs if not present on system.
"""
with settings(warn_only=True):
result = env.safe_run("make")
# no ncurses, fix Makefile and rebuild
if result.failed:
env.safe_sed("Makefile", "-D_CURSES_LIB=1", "-D_CURSES_LIB=0")
env.safe_sed("Makefile", "-lcurses", "# -lcurses")
env.safe_run("make clean")
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
for fname in env.safe_run_output("ls -1 samtools bcftools/bcftools bcftools/vcfutils.pl misc/wgsim").split("\n"):
env.safe_sudo("cp -f %s %s" % (fname.rstrip("\r"), install_dir))
def install_blast(env):
version = env.tool_version
url = 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%s/ncbi-blast-%s-x64-linux.tar.gz' % (version[:-1], version)
install_dir = env.system_install
install_cmd = sudo if env.use_sudo else run
if not exists(install_dir):
install_cmd("mkdir -p %s" % install_dir)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
run("tar -xvzf %s" % os.path.split(url)[-1])
with cd('ncbi-blast-%s/bin' % version):
bin_dir = _get_bin_dir(env)
install_cmd("mv * '%s'" % bin_dir)
def install_blast(env):
version = env.tool_version
url = 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%s/ncbi-blast-%s-x64-linux.tar.gz' % (version[:-1], version)
install_dir = env.system_install
install_cmd = env.safe_sudo if env.use_sudo else env.safe_run
if not env.safe_exists(install_dir):
install_cmd("mkdir -p %s" % install_dir)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % url)
env.safe_run("tar -xvzf %s" % os.path.split(url)[-1])
with cd('ncbi-blast-%s/bin' % version):
bin_dir = _get_bin_dir(env)
install_cmd("mv * '%s'" % bin_dir)
def _safe_ncurses_make(env):
"""Combine samtools, removing ncurses refs if not present on system.
"""
with settings(warn_only=True):
result = env.safe_run("make")
# no ncurses, fix Makefile and rebuild
if result.failed:
env.safe_sed("Makefile", "-D_CURSES_LIB=1", "-D_CURSES_LIB=0")
env.safe_sed("Makefile", "-lcurses", "# -lcurses")
env.safe_run("make clean")
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
for fname in env.safe_run_output("ls -1 samtools bcftools/bcftools bcftools/vcfutils.pl misc/wgsim").split("\n"):
env.safe_sudo("cp -f %s %s" % (fname.rstrip("\r"), install_dir))
def install_novosort(env):
"""Multithreaded sort and merge for BAM files.
http://www.novocraft.com/wiki/tiki-index.php?page=Novosort
"""
base_version = "V3.00.02"
version = "V1.00.02"
url = "http://www.novocraft.com/downloads/%s/novosort%s.gcc.tar.gz" % (base_version, version)
ref_url = "http://www.novocraft.com/main/downloadpage.php"
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, url)
env.safe_run("tar -xzvpf novosort%s.gcc.tar.gz" % version)
with cd("novosort"):
for fname in ["novosort"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def install_novosort(env):
"""Multithreaded sort and merge for BAM files.
http://www.novocraft.com/wiki/tiki-index.php?page=Novosort
"""
base_version = "V3.00.02"
version = "V1.00.02"
url = "http://www.novocraft.com/downloads/%s/novosort%s.gcc.tar.gz" % (base_version, version)
ref_url = "http://www.novocraft.com/main/downloadpage.php"
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_wget_with_cookies(ref_url, url)
env.safe_run("tar -xzvpf novosort%s.gcc.tar.gz" % version)
with cd("novosort"):
for fname in ["novosort"]:
env.safe_sudo("mv %s %s" % (fname, install_dir))
def _freenx_scripts(env):
"""Provide graphical access to clients via FreeNX.
"""
home_dir = env.safe_run_output("echo $HOME")
setup_script = "setupnx.sh"
bin_dir = shared._get_bin_dir(env)
install_file_dir = os.path.join(env.config_dir, os.pardir, "installed_files")
if not env.safe_exists(os.path.join(bin_dir, setup_script)):
env.safe_put(os.path.join(install_file_dir, setup_script),
os.path.join(home_dir, setup_script))
env.safe_run("chmod 0777 %s" % os.path.join(home_dir, setup_script))
env.safe_sudo("mv %s %s" % (os.path.join(home_dir, setup_script), bin_dir))
remote_login = "******"
if not env.safe_exists(os.path.join(home_dir, remote_login)):
env.safe_put(os.path.join(install_file_dir, 'bash_login'), os.path.join(home_dir, remote_login))
env.safe_run("chmod 0777 %s" % os.path.join(home_dir, remote_login))
_configure_gnome(env)
def install_pgdspider(env):
"""PGDSpider format conversion for population genetics programs.
http://www.cmpg.unibe.ch/software/PGDSpider/
"""
if os.path.exists(os.path.join(shared._get_bin_dir(env), "PGDSpider2.sh")):
return
version = "2.0.2.0"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
v=version)
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = shared._get_bin_dir(env)
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
env.safe_run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
_java_install("PGDSpider", version, url, env, install_fn=_install_fn)
def _freenx_scripts(env):
"""Provide graphical access to clients via FreeNX.
"""
home_dir = env.safe_run_output("echo $HOME")
setup_script = "setupnx.sh"
bin_dir = shared._get_bin_dir(env)
install_file_dir = os.path.join(env.config_dir, os.pardir,
"installed_files")
if not env.safe_exists(os.path.join(bin_dir, setup_script)):
env.safe_put(os.path.join(install_file_dir, setup_script),
os.path.join(home_dir, setup_script))
env.safe_run("chmod 0777 %s" % os.path.join(home_dir, setup_script))
env.safe_sudo("mv %s %s" %
(os.path.join(home_dir, setup_script), bin_dir))
remote_login = "******"
if not env.safe_exists(os.path.join(home_dir, remote_login)):
env.safe_put(os.path.join(install_file_dir, 'bash_login'),
os.path.join(home_dir, remote_login))
env.safe_run("chmod 0777 %s" % os.path.join(home_dir, remote_login))
_configure_gnome(env)
def install_pgdspider(env):
"""PGDSpider format conversion for population genetics programs.
http://www.cmpg.unibe.ch/software/PGDSpider/
"""
if os.path.exists(os.path.join(shared._get_bin_dir(env), "PGDSpider2.sh")):
return
version = "2.0.2.0"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
v=version)
def _install_fn(env, install_dir):
env.safe_sudo("mv *.jar %s" % install_dir)
bin_dir = shared._get_bin_dir(env)
exe_file = "PGDSpider2.sh"
jar = "PGDSpider2.jar"
env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir,
jar=jar))
env.safe_run("chmod a+x {0}".format(exe_file))
env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
_java_install("PGDSpider", version, url, env, install_fn=_install_fn)
def _build(env):
with cd("pbgzip"):
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
env.safe_sudo("cp -f pbgzip %s" % (install_dir))
def install_biokepler(env):
url = "http://www.biokepler.org/files/downloads/biokepler-1.0.deb"
tool = url[url.rfind('/')+1:]
_download_install_deb_pkg(env, url, tool)
install_dir = shared._get_bin_dir(env)
env.safe_sudo("ln -f -s /opt/kepler/biokepler-1.0/kepler.sh %s/kepler" % install_dir)
def _build(env):
with cd("pbgzip"):
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
env.safe_sudo("cp -f pbgzip %s" % (install_dir))