Mercurial > repos > fubar > differential_count_models
view tool_dependencies.xml @ 28:c4ee2e69d691 draft
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author | fubar |
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date | Wed, 07 Aug 2013 02:41:40 -0400 |
parents | c0fa3dde02d9 |
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<?xml version="1.0"?> <tool_dependency> <package name="r3" version="3.0.1"> <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package>package_ghostscript_9_07 <package name="ghostscript" version="9.07"> <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="graphicsmagick" version="1.3.18"> <repository changeset_revision="50d546dfd6b9" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="biocbasics" version="2.12"> <install version="1.0"> <actions> <action type="set_environment_for_install"> <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> <package name="r3" version="3.0.1" /> </repository> </action> <action type="make_directory">$INSTALL_DIR</action> <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> </actions> </install> <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs It's clunky but this is the most convenient way I could get anything installed into the package_r3 Note we use cran at fred hutch since no fastest mirror thingy </readme> </package> </tool_dependency>