Python _pip_cmd Examples

Example #1

File: bio_nextgen.py Project: kevyin/cloudbiolinux

 def _gemini_install(env):
     env.safe_sudo("{0} install --upgrade cython".format(_pip_cmd(env)))
     env.safe_sudo("{0} install --upgrade distribute".format(_pip_cmd(env)))
     _python_make(env)
     env.safe_sudo("mkdir -p {0}".format(data_dir))
     env.safe_sudo("chown {0} {1}".format(env.user, data_dir))
     run("python{0} gemini/install-data.py {1}".format(env.python_version_ext, data_dir))
     env.safe_sudo("rm -rf gemini.egg-info")

Example #2

File: python.py Project: Ykay007/cloudbiolinux

def install_bx_python(env):
    """Tools for manipulating biological data, particularly multiple sequence alignments
    https://bitbucket.org/james_taylor/bx-python/wiki/Home
    """
    version = "bitbucket"
    url = "https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2"
    env.safe_sudo("%s install --upgrade distribute" % _pip_cmd(env))
    env.safe_sudo("%s install --upgrade %s" % (_pip_cmd(env), url))

Example #3

File: python.py Project: Traksewt/cloudbiolinux

def install_bx_python(env):
    """Tools for manipulating biological data, particularly multiple sequence alignments
    https://bitbucket.org/james_taylor/bx-python/wiki/Home
    """
    version = "bitbucket"
    url = "https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2"
    env.safe_sudo("%s install --upgrade distribute" % _pip_cmd(env))
    env.safe_sudo("%s install --upgrade %s" % (_pip_cmd(env), url))

Example #4

File: python.py Project: janusz005/cloudbiolinux

def install_netsa_python(env):
    """A suite of open source tools for monitoring large-scale networks using flow data.
    http://tools.netsa.cert.org/index.html
    """
    version = "1.3"
    url = "http://tools.netsa.cert.org/releases/netsa-python-%s.tar.gz" % version
    env.safe_sudo("%s install %s" % (_pip_cmd(env), url))

Example #5

File: python.py Project: janusz005/cloudbiolinux

def install_netsa_python(env):
    """A suite of open source tools for monitoring large-scale networks using flow data.
    http://tools.netsa.cert.org/index.html
    """
    version = "1.3"
    url = "http://tools.netsa.cert.org/releases/netsa-python-%s.tar.gz" % version
    env.safe_sudo("%s install %s" % (_pip_cmd(env), url))

Example #6

File: distributed.py Project: clsung/cloudbiolinux

def install_pydoop(env):
    """pydoop; provides Hadoop access for Python.
    http://pydoop.sourceforge.net/docs/
    """
    java_home = env.java_home if env.has_key("java_home") else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    env.safe_sudo("%s && %s install pydoop" % (export_str, _pip_cmd(env)))

Example #7

def install_pydoop(env):
    """pydoop; provides Hadoop access for Python.
    http://pydoop.sourceforge.net/docs/
    """
    java_home = env.java_home if env.has_key("java_home") else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    env.safe_sudo("%s && %s install pydoop" % (export_str, _pip_cmd(env)))

Example #8

def install_pydoop(env):
    """pydoop; provides Hadoop access for Python.
    http://pydoop.sourceforge.net/docs/
    """
    java_home = env.java_home if "java_home" in env else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    cmd = env.safe_run if _is_anaconda(env) else env.safe_sudo
    cmd("%s && %s install pydoop" % (export_str, _pip_cmd(env)))

Example #9

File: distributed.py Project: Altoros/cloudbiolinux

def install_pydoop(env):
    """pydoop; provides Hadoop access for Python.
    http://pydoop.sourceforge.net/docs/
    """
    java_home = env.java_home if "java_home" in env else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    cmd = env.safe_run if _is_anaconda(env) else env.safe_sudo
    cmd("%s && %s install pydoop" % (export_str, _pip_cmd(env)))

Example #10

File: distributed.py Project: clsung/cloudbiolinux

def install_seal(env):
    """Install seal: process high-throughput sequencing with Hadoop.

    http://biodoop-seal.sf.net/
    """
    install_pydoop(env)

    java_home = env.java_home if env.has_key("java_home") else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    env.safe_sudo("%s && %s install seal" % (export_str, _pip_cmd(env)))

Example #11

def install_seal(env):
    """Install seal: process high-throughput sequencing with Hadoop.

    http://biodoop-seal.sf.net/
    """
    install_pydoop(env)

    java_home = env.java_home if env.has_key("java_home") else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    env.safe_sudo("%s && %s install seal" % (export_str, _pip_cmd(env)))

Example #12

def install_seal(env):
    """Install seal: process high-throughput sequencing with Hadoop.

    http://biodoop-seal.sf.net/
    """
    install_pydoop(env)

    java_home = env.java_home if "java_home" in env else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    cmd = env.safe_run if _is_anaconda(env) else env.safe_sudo
    cmd("%s && %s install --pre seal" % (export_str, _pip_cmd(env)))

Example #13

File: distributed.py Project: Altoros/cloudbiolinux

def install_seal(env):
    """Install seal: process high-throughput sequencing with Hadoop.

    http://biodoop-seal.sf.net/
    """
    install_pydoop(env)

    java_home = env.java_home if "java_home" in env else os.environ["JAVA_HOME"]
    export_str = "export JAVA_HOME=%s" % (java_home)
    cmd = env.safe_run if _is_anaconda(env) else env.safe_sudo
    cmd("%s && %s install --pre seal" % (export_str, _pip_cmd(env)))