Python _get_bin_dir Examples

Example #1

File: bio_nextgen.py Project: logston/cloudbiolinux

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)

Example #2

File: bio_nextgen.py Project: Traksewt/cloudbiolinux

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)

Example #3

File: bio_proteomics.py Project: janusz005/cloudbiolinux

 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)

Example #4

File: bio_nextgen.py Project: nldowell/cloudbiolinux

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)

Example #5

 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)

Example #6

File: bio_proteomics_wine.py Project: Altoros/cloudbiolinux

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')

Example #7

 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)

Example #8

File: bio_proteomics_wine.py Project: janusz005/cloudbiolinux

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)

Example #9

File: bio_proteomics.py Project: janusz005/cloudbiolinux

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)

Example #10

File: bio_proteomics.py Project: janusz005/cloudbiolinux

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)

Example #11

File: bio_proteomics.py Project: ny-shao/cloudbiolinux

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)

Example #12

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)

Example #13

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)

Example #14

 def _move(env):
     bin_dir = _get_bin_dir(env)
     env.safe_sudo("mv bin/* '%s'" % (bin_dir))

Example #15

File: bio_proteomics.py Project: janusz005/cloudbiolinux

 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)

Example #16

File: bio_proteomics.py Project: janusz005/cloudbiolinux

 def _move(env):
     bin_dir = _get_bin_dir(env)
     env.safe_sudo("mv bin/* '%s'" % (bin_dir, bin_dir))