| Previous changeset 38:ba361e7ebc17 (2013-06-13) Next changeset 40:5c211b875782 (2013-06-13) |
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rgedgeR/tool_dependencies.xml |
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| diff -r ba361e7ebc17 -r d110c5bb0ad3 rgedgeR/tool_dependencies.xml --- a/rgedgeR/tool_dependencies.xml Thu Jun 13 01:09:25 2013 -0400 +++ b/rgedgeR/tool_dependencies.xml Thu Jun 13 01:36:22 2013 -0400 |
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| @@ -11,7 +11,12 @@ <package name="r3" version="3.0.1" /> </repository> </action> - <action type="shell_command">R CMD BATCH rgedgeR/installBioC.R </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) >> $INSTALL_DIR/runme.R</action> + <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> </actions> </install> <readme>Installs some basic bioc packages for the edgeR tool |