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installers.py
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def get_clone_s3turbo_repo_commands(targetdir='.'):
commands = ['eval `ssh-agent`; ssh-add; cd %s; git clone -q [email protected]:deaconjs/s3turbo.git'%(targetdir)]
return commands
def get_trimmomatic_repo_commands():
commands = ['wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.35.zip; unzip Trimmomatic-0.35.zip']
return commands
def get_fastqc_commands():
commands = ['eb --filter-deps=Java fastqc-0.11.3.eb --robot']
return commands
def get_samtools_commands():
commands = ['eb ncurses-5.9-goolf-1.4.10.eb --robot; eb SAMtools-1.2-goolf-1.7.20.eb --robot']
return commands
def get_easybuild_commands(package=None):
commands = []
if package:
commands = ['eb --filter-deps=Java %s --robot'%(package)]
return commands
def install_R():
commands = ['sudo yum -yq install libpng-devel.x86_64 R']
return commands
def install_bioconductor():
commands = install_R()
commands.append("sudo R -e 'source(\"https://bioconductor.org/biocLite.R\")'")
return commands
def install_lumi():
commands = install_R()
commands.append("sudo yum -y install openssl-devel libxml2-devel.x86_64 libcurl-devel")
commands.append("sudo R -e 'source(\"https://bioconductor.org/biocLite.R\"); biocLite(\"RCurl\"); biocLite(\"methylumi\")'")
#commands.append("sudo R -e 'biocLite(\"methylumi\")'")
return commands
def install_picard():
commands = []
commands.append("cd tools; wget https://github.com/broadinstitute/picard/releases/download/2.5.0/picard-tools-2.5.0.zip; unzip picard-tools-2.5.0.zip; rm picard-tools-2.5.0.zip")
return commands
def install_rnbeads():
commands = install_R()
commands.append("sudo yum -y install openssl-devel libxml2-devel.x86_64 libcurl-devel ghostscript-devel.i686")
commands.append("sudo R -e 'source(\"https://bioconductor.org/biocLite.R\"); biocLite(\"qvalue\")'")
commands.append("sudo R -e 'install.packages(\"isva\", repos=\"http://cran.uk.r-project.org\")'")
commands.append("sudo R -e 'install.packages(\"ff\", repos=\"http://cran.uk.r-project.org\")'")
commands.append("sudo R -e 'source(\"https://bioconductor.org/biocLite.R\"); biocLite(\"survival\", ask=FALSE); biocLite(\"nlme\"); biocLite(\"Repitools\"); biocLite(\"RnBeads\"); biocLite(\"RnBeads.hg19\")'")
return commands