# HG changeset patch # User fubar # Date 1393819657 18000 # Node ID 395197c30bf7e8fa9dfbc3c4242ab384e3f3d467 # Parent e7d02e6b253c215466d5d7cb26eb133f62ae8cbf Uploaded diff -r e7d02e6b253c -r 395197c30bf7 tool_dependencies.xml --- a/tool_dependencies.xml Sun Mar 02 23:01:19 2014 -0500 +++ b/tool_dependencies.xml Sun Mar 02 23:07:37 2014 -0500 @@ -20,9 +20,12 @@ <package name="r303" version="3.0.3" /> </repository> </action> - <action type="make_directory">$INSTALL_DIR</action> - <action type="shell_command">ls -l</action> - <action type="shell_command">export PATH=$PATH && R CMD BATCH $RUNME_PATH/runme.R </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="move_file"> + <source>">$REPOSITORY_INSTALL_DIR/runme.R</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="shell_command">export PATH=$PATH && 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