# HG changeset patch
# User fubar
# Date 1371102714 14400
# Node ID 4afd763390e6982a16961831405937d776c355a4
# Parent 5c211b87578224be93d796c8417ded7b358a138a
Uploaded
diff -r 5c211b875782 -r 4afd763390e6 rgedgeR/installBioC.R
--- a/rgedgeR/installBioC.R Thu Jun 13 01:41:21 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-source('http://bioconductor.org/biocLite.R')
-installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')
-biocLite()
-biocLite(installme)
diff -r 5c211b875782 -r 4afd763390e6 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml Thu Jun 13 01:41:21 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml Thu Jun 13 01:51:54 2013 -0400
@@ -16,12 +16,12 @@
echo "installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')" >> $INSTALL_DIR/runme.R
echo "biocLite()" >> $INSTALL_DIR/runme.R
echo "biocLite(installme)" >> $INSTALL_DIR/runme.R
- echo "quit(save='no')" >> $INSTALL_DIR/runme.R
-
+ echo "quit(save='no')" >> $INSTALL_DIR/runme.R
export PATH=$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 tool
+ 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