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")
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))
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))
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)))
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)))
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)))
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)))