# HG changeset patch # User fubar # Date 1392703948 18000 # Node ID a83f8effff05bbfb6bb06414f1a8766499d19550 # Parent f33aac17f15d563203b8013e865d2118c87252de Uploaded diff -r f33aac17f15d -r a83f8effff05 tool_dependencies.xml --- a/tool_dependencies.xml Tue Feb 18 01:12:00 2014 -0500 +++ b/tool_dependencies.xml Tue Feb 18 01:12:28 2014 -0500 @@ -24,8 +24,8 @@ echo "biocLite(installme)" >> $INSTALL_DIR/runme.R echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R echo "quit(save='no')" >> $INSTALL_DIR/runme.R - echo "PATH=$PATH" - export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R + echo "PATH=$PATH" + export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs