Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 102:851f3946c9d9 draft
Uploaded
| author | fubar |
|---|---|
| date | Sun, 02 Mar 2014 23:20:48 -0500 |
| parents | df7ce9396d86 |
| children | 83dc8bc30254 |
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| 101:df7ce9396d86 | 102:851f3946c9d9 |
|---|---|
| 15 <action type="set_environment_for_install"> | 15 <action type="set_environment_for_install"> |
| 16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 17 <package name="r303" version="3.0.3" /> | 17 <package name="r303" version="3.0.3" /> |
| 18 </repository> | 18 </repository> |
| 19 </action> | 19 </action> |
| 20 <action type="make_directory">$INSTALL_DIR</action> | 20 <action type="make_directory">$INSTALL_DIR</action> |
| 21 <action type="move_file"> | 21 <action type="shell_command">echo 'bioclite = "http://bioconductor.org/biocLite.R"' > $INSTALL_DIR/runme.R</action> |
| 22 <source>runme.R</source> | 22 <action type="shell_command">echo "source(bioclite)" >> $INSTALL_DIR/runme.R</action> |
| 23 <destination>$INSTALL_DIR</destination> | 23 <action type="shell_command">echo 'installme=c("edgeR","limma","DESeq","DESeq2")' >> $INSTALL_DIR/runme.R</action> |
| 24 </action> | 24 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> |
| 25 <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action> | 25 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> |
| 26 <action type="shell_command">echo 'install.packages(c("stringr","gplots"),dependencies=T,repos="http://cran.us.r-project.org")' >> $INSTALL_DIR/runme.R</action> | |
| 27 <action type="shell_command">echo 'quit(save="no")' >> $INSTALL_DIR/runme.R</action> | |
| 28 <action type="shell_command">echo "PATH=$PATH 1>&2"</action> | |
| 29 <action type="shell_command">echo "R_PATH=$R_PATH 1>&2"</action> | |
| 30 <action type="shell_command">export PATH=$PATH && $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action> | |
| 26 </actions> | 31 </actions> |
| 27 </install> | 32 </install> |
| 28 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs | 33 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs |
| 29 It's clunky but this is the most convenient way I could get anything installed into the package_r3 | 34 It's clunky but this is the most convenient way I could get anything installed into the package_r3 |
| 30 Note we use cran at fred hutch since no fastest mirror thingy | 35 Note we use cran at fred hutch since no fastest mirror thingy |