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fake_modules.py
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from starcluster.clustersetup import ClusterSetup
from starcluster.logger import log
class FakeModInstaller(ClusterSetup):
def run(self, nodes, master, user, user_shell, volumes):
for node in nodes:
log.info("Creating python 2.6.5 module files on %s" % (node.alias))
node.ssh.execute('mkdir /usr/local/Modules/applications/python')
node.ssh.execute('echo "#%Module" >> /usr/local/Modules/applications/python/2.6.5')
node.ssh.execute('echo "set root /usr/bin/python" >> /usr/local/Modules/applications/python/2.6.5')
node.ssh.execute('echo -e "prepend-path\tPATH\t\$root/bin" >> /usr/local/Modules/applications/python/2.6.5')
log.info("Creating python 2.7.4 module files on %s" % (node.alias))
node.ssh.execute('echo "#%Module" >> /usr/local/Modules/applications/python/2.7.4')
node.ssh.execute('echo "set root /usr/bin/python" >> /usr/local/Modules/applications/python/2.7.4')
node.ssh.execute('echo -e "prepend-path\tPATH\t\$root/bin" >> /usr/local/Modules/applications/python/2.7.4')
log.info("Creating GATK 3.2-2 module files on %s" % (node.alias))
node.ssh.execute('mkdir /usr/local/Modules/applications/gatk')
node.ssh.execute('echo "#%Module" >> /usr/local/Modules/applications/gatk/3.2-2')
node.ssh.execute('echo "set root /opt/software/gatk/3.2-2" >> /usr/local/Modules/applications/gatk/3.2-2')
node.ssh.execute('echo -e "prepend-path\tPATH\t\$root" >> /usr/local/Modules/applications/gatk/3.2-2')
node.ssh.execute('mkdir -p /opt/software/gatk/3.2-2')
log.info("Creating GATK 3.3-0 module files on %s" % (node.alias))
node.ssh.execute('mkdir /usr/local/Modules/applications/gatk')
node.ssh.execute('echo "#%Module" >> /usr/local/Modules/applications/gatk/3.3-0')
node.ssh.execute('echo "set root /opt/software/gatk/3.3-0" >> /usr/local/Modules/applications/gatk/3.3-0')
node.ssh.execute('echo -e "prepend-path\tPATH\t\$root" >> /usr/local/Modules/applications/gatk/3.3-0')
node.ssh.execute('mkdir -p /opt/software/gatk/3.3-0')
log.info("Creating GATK 3.5-0 module files on %s" % (node.alias))
node.ssh.execute('mkdir /usr/local/Modules/applications/gatk')
node.ssh.execute('echo "#%Module" >> /usr/local/Modules/applications/gatk/3.5-0')
node.ssh.execute('echo "set root /opt/software/gatk/3.5-0" >> /usr/local/Modules/applications/gatk/3.5-0')
node.ssh.execute('echo -e "prepend-path\tPATH\t\$root" >> /usr/local/Modules/applications/gatk/3.5-0')
node.ssh.execute('mkdir -p /opt/software/gatk/3.5-0')
log.info("Creating MuTect 1.1.4 module files on %s" % (node.alias))
node.ssh.execute('mkdir /usr/local/Modules/applications/mutect')
node.ssh.execute('echo "#%Module" >> /usr/local/Modules/applications/mutect/1.1.4')
node.ssh.execute('echo "set root /opt/software/mutect/1.1.4" >> /usr/local/Modules/applications/mutect/1.1.4')
node.ssh.execute('echo -e "prepend-path\tPATH\t\$root" >> /usr/local/Modules/applications/mutect/1.1.4')
node.ssh.execute('mkdir -p /opt/software/mutect/1.1.4')