Mercurial > repos > fubar > edger_test
changeset 41:4afd763390e6 draft
Uploaded
author | fubar |
---|---|
date | Thu, 13 Jun 2013 01:51:54 -0400 |
parents | 5c211b875782 |
children | 697272b8ef42 |
files | rgedgeR/installBioC.R rgedgeR/tool_dependencies.xml |
diffstat | 2 files changed, 3 insertions(+), 7 deletions(-) [+] |
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--- 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)
--- 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 @@ <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">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> - + <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command"> export PATH=$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 + <readme>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 </readme> </package> </tool_dependency>