def _download_executables(env, base_url, tools):
install_dir = _get_bin_dir(env)
for tool in tools:
with cd(install_dir):
if not exists(tool):
env.safe_sudo("wget %s%s" % (base_url, tool))
env.safe_sudo("chmod a+rwx %s" % tool)
def _download_executables(env, base_url, tools):
install_dir = _get_bin_dir(env)
for tool in tools:
with cd(install_dir):
if not exists(tool):
env.safe_sudo("wget %s%s" % (base_url, tool))
env.safe_sudo("chmod a+rwx %s" % tool)
def install_fn(env, install_dir):
share_dir = _get_install_subdir(env, "share")
env.safe_sudo("mv Mayu '%s'" % share_dir)
bin_dir = _get_bin_dir(env)
executable = "%s/Mayu" % bin_dir
env.safe_sudo("""echo '#!/bin/bash\ncd %s/Mayu; perl Mayu.pl \"$@\"' > %s """ % (share_dir, executable))
env.safe_sudo("chmod +x '%s'" % executable)
def install_ucsc_tools(env):
"""Useful executables from UCSC.
todo: install from source to handle 32bit and get more programs
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
"""
tools = [
"liftOver",
"faToTwoBit",
"bedToBigBed",
"bigBedInfo",
"bigBedSummary",
"bigBedToBed",
"bigWigInfo",
"bigWigSummary",
"bigWigToBedGraph",
"bigWigToWig",
"fetchChromSizes",
"wigToBigWig",
"faSize",
"twoBitInfo",
"faCount",
]
url = "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/"
install_dir = _get_bin_dir(env)
for tool in tools:
with cd(install_dir):
if not exists(tool):
env.safe_sudo("wget %s%s" % (url, tool))
env.safe_sudo("chmod a+rwx %s" % tool)
def install_fn(env, install_dir):
share_dir = _get_install_subdir(env, "share")
env.safe_sudo("mv Mayu '%s'" % share_dir)
bin_dir = _get_bin_dir(env)
executable = "%s/Mayu" % bin_dir
env.safe_sudo(
"""echo '#!/bin/bash\ncd %s/Mayu; perl Mayu.pl \"$@\"' > %s """ %
(share_dir, executable))
env.safe_sudo("chmod +x '%s'" % executable)
def setup_wine_wrapper(env, to):
basename = os.path.basename(to)
contents = """#!/bin/bash
setup_proteomics_wine_env.sh
export WINEPREFIX=$HOME/.wine-proteomics
wine %s "$@"
""" % to
bin_dir = _get_bin_dir(env)
dest = "%s/%s" % (bin_dir, basename)
_write_to_file(contents, dest, '0755')
def install_fn(env, install_dir):
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = _get_bin_dir(env)
for script in [
"ITraqScanSummarizer", "LTQ-iQuant", "LTQ-iQuant-cli",
"MgfFormatter"
]:
env.safe_sudo("ln -s '%s' %s" %
(os.path.join(install_dir, script), bin_dir))
env.safe_sudo("chmod +x '%s'/*" % bin_dir)
def setup_wine_wrapper(env, to):
basename = os.path.basename(to)
contents = """#!/bin/bash
setup_proteomics_wine_env.sh
export WINEPREFIX=$HOME/.wine-proteomics
wine %s "$@"
""" % to
bin_dir = _get_bin_dir(env)
dest = "%s/%s" % (bin_dir, basename)
_write_to_file(contents, dest, 0755)
def install_ms2preproc(env):
default_version = "2009"
version = env.get("tool_version", default_version)
get_cmd = 'wget --post-data "Anonym=1&GotoDownload=1&ref=http://hci.iwr.uni-heidelberg.de/MIP/Software/ms2preproc.php" http://hci.iwr.uni-heidelberg.de/php-tools/download.php -O ms2preproc.zip'
install_dir = _get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run(get_cmd)
run("unzip ms2preproc.zip")
run("chmod +x ms2preproc-x86_64")
env.safe_sudo("mv ms2preproc-x86_64 '%s'/ms2preproc" % install_dir)
def install_ms2preproc(env):
default_version = "2009"
version = env.get("tool_version", default_version)
get_cmd = 'wget --post-data "Anonym=1&GotoDownload=1&ref=http://hci.iwr.uni-heidelberg.de/MIP/Software/ms2preproc.php" http://hci.iwr.uni-heidelberg.de/php-tools/download.php -O ms2preproc.zip'
install_dir = _get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run(get_cmd)
run("unzip ms2preproc.zip")
run("chmod +x ms2preproc-x86_64")
env.safe_sudo("mv ms2preproc-x86_64 '%s'/ms2preproc" % install_dir)
def install_ms2preproc(env):
default_version = "2009"
version = env.get("tool_version", default_version)
get_cmd = 'wget "http://software.steenlab.org/ms2preproc/ms2preproc.zip" -O ms2preproc.zip'
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run(get_cmd)
env.safe_run("unzip ms2preproc.zip")
with cd("ms2preproc"):
env.safe_run("mv ms2preproc-r2821-x86_64 ms2preproc-x86_64")
env.safe_run("chmod +x ms2preproc-x86_64")
install_dir = _get_bin_dir(env)
env.safe_sudo("mv ms2preproc-x86_64 '%s'/ms2preproc" % install_dir)
def install_ms2preproc(env):
default_version = "2009"
version = env.get("tool_version", default_version)
get_cmd = 'wget "http://software.steenlab.org/ms2preproc/ms2preproc.zip" -O ms2preproc.zip'
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run(get_cmd)
env.safe_run("unzip ms2preproc.zip")
with cd("ms2preproc"):
env.safe_run("mv ms2preproc-r2821-x86_64 ms2preproc-x86_64")
env.safe_run("chmod +x ms2preproc-x86_64")
install_dir = _get_bin_dir(env)
env.safe_sudo("mv ms2preproc-x86_64 '%s'/ms2preproc" %
install_dir)
def install_ucsc_tools(env):
"""Useful executables from UCSC.
todo: install from source to handle 32bit and get more programs
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
"""
tools = ["liftOver", "faToTwoBit", "bedToBigBed",
"bigBedInfo", "bigBedSummary", "bigBedToBed",
"bigWigInfo", "bigWigSummary", "bigWigToBedGraph", "bigWigToWig",
"fetchChromSizes", "wigToBigWig", "faSize", "twoBitInfo",
"faCount"]
url = "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/"
install_dir = _get_bin_dir(env)
for tool in tools:
with cd(install_dir):
if not exists(tool):
env.safe_sudo("wget %s%s" % (url, tool))
env.safe_sudo("chmod a+rwx %s" % tool)
def _move(env):
bin_dir = _get_bin_dir(env)
env.safe_sudo("mv bin/* '%s'" % (bin_dir))
def install_fn(env, install_dir):
env.safe_sudo("mv * '%s'" % install_dir)
bin_dir = _get_bin_dir(env)
for script in ["ITraqScanSummarizer", "LTQ-iQuant", "LTQ-iQuant-cli", "MgfFormatter"]:
env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, script), bin_dir))
env.safe_sudo("chmod +x '%s'/*" % bin_dir)
def _move(env):
bin_dir = _get_bin_dir(env)
env.safe_sudo("mv bin/* '%s'" % (bin_dir, bin_dir))