Mercurial > repos > fubar > differential_count_models
diff tool_dependencies.xml @ 53:b608991544f5 draft
Uploaded
| author | fubar |
|---|---|
| date | Sun, 09 Feb 2014 19:04:12 -0500 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Feb 09 19:04:12 2014 -0500 @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="r3" version="3.0.2"> + <repository changeset_revision="1415ab68e93e" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package>package_ghostscript_9_07 + <package name="ghostscript" version="9.10"> + <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="biocbasics" version="2.14"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="1415ab68e93e" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="r3" version="3.0.2" /> + </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>