| Previous changeset 92:71ba9cdc9838 (2014-03-02) Next changeset 94:9414bbf5579b (2014-03-02) |
|
Commit message:
Uploaded |
|
modified:
tool_dependencies.xml |
| b |
| diff -r 71ba9cdc9838 -r 34ef458b7fd9 tool_dependencies.xml --- a/tool_dependencies.xml Sun Mar 02 22:21:47 2014 -0500 +++ b/tool_dependencies.xml Sun Mar 02 22:25:13 2014 -0500 |
| b |
| @@ -17,17 +17,8 @@ <package name="r303" version="3.0.3" /> </repository> </action> - <action type="make_directory">$INSTALL_DIR</action> - <action type="shell_command">echo "bioclite = 'http://bioconductor.org/biocLite.R'" > $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "source(bioclite)" >> $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')" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "PATH=$PATH 1>&2"</action> - <action type="shell_command">echo "R_PATH=$R_PATH 1>&2"</action> - <action type="shell_command">export PATH=$PATH && $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">export PATH=$PATH && R CMD BATCH 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 |