Mercurial > repos > fubar > differential_count_models
diff tool_dependencies.xml @ 32:8051d14cf819 draft
update with better filtering
| author | fubar |
|---|---|
| date | Sun, 22 Dec 2013 01:32:29 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Dec 22 01:32:29 2013 -0500 @@ -0,0 +1,29 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="package_r3" version="3.0.1"> + <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" 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="6344ee60d0cf" 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','DEXSeq','ggplot2','gplots')" >> $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 "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 > $INSTALL_DIR/install.log </action> + <action type="shell_command">cat $INSTALL_DIR/install.log</action> + </actions> + </install> + <readme>Installs some basic bioc packages for the edgeR wrapper + It's clunky but this is the only way I could get anything installed into the package_r3 R + </readme> + </package> +</tool_dependency>