# HG changeset patch # User yhoogstrate # Date 1441033202 14400 # Node ID acb56603b268d4166223fb488352a25cb1be0c10 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae diff -r 000000000000 -r acb56603b268 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Aug 31 11:00:02 2015 -0400 @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + $INSTALL_DIR + echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R + echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R + echo "biocLite()" >> $INSTALL_DIR/runme.R + echo "biocLite(installme)" >> $INSTALL_DIR/runme.R + echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $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 the latest bioc packages: edgeR & Limma + + + + + + + mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/ + + $INSTALL_DIR/bin/design_matrix_creator + + + $INSTALL_DIR/bin + $REPOSITORY_INSTALL_DIR + + + + + + + + + mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/ + + $INSTALL_DIR/bin/edger_dge_table_to_bedgraph + + + $INSTALL_DIR/bin + $REPOSITORY_INSTALL_DIR + + + + +