| Previous changeset 101:df7ce9396d86 (2014-03-02) Next changeset 103:83dc8bc30254 (2014-03-02) |
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Commit message:
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modified:
tool_dependencies.xml |
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| diff -r df7ce9396d86 -r 851f3946c9d9 tool_dependencies.xml --- a/tool_dependencies.xml Sun Mar 02 23:10:55 2014 -0500 +++ b/tool_dependencies.xml Sun Mar 02 23:20:48 2014 -0500 |
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| @@ -17,12 +17,17 @@ <package name="r303" version="3.0.3" /> </repository> </action> - <action type="make_directory">$INSTALL_DIR</action> - <action type="move_file"> - <source>runme.R</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action> + <action type="make_directory">$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> </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 |