Mercurial > repos > fubar > differential_count_models
comparison rgedgeR/tool_dependencies.xml @ 1:df4fea3be1b3 draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 27 Jul 2013 00:17:06 -0400 |
| parents | 2122e630b13a |
| children | fe5c828dee80 |
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| 0:2122e630b13a | 1:df4fea3be1b3 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="r3" version="3.0.1"> | 3 <package name="r3" version="3.0.1"> |
| 4 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 4 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 5 </package>package_ghostscript_9_07 | |
| 6 <package name="ghostscript" version="9.07"> | |
| 7 <repository changeset_revision="0cdd8d3ffebc" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | |
| 8 </package> | |
| 9 <package name="graphicsmagick" version="1.3"> | |
| 10 <repository changeset_revision="50d546dfd6b9" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | |
| 5 </package> | 11 </package> |
| 6 <package name="biocbasics" version="2.12"> | 12 <package name="biocbasics" version="2.12"> |
| 7 <install version="1.0"> | 13 <install version="1.0"> |
| 8 <actions> | 14 <actions> |
| 9 <action type="set_environment_for_install"> | 15 <action type="set_environment_for_install"> |
| 14 <action type="make_directory">$INSTALL_DIR</action> | 20 <action type="make_directory">$INSTALL_DIR</action> |
| 15 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> | 21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> |
| 16 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> | 22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> |
| 17 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> | 23 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> |
| 18 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> | 24 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> |
| 19 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" >> $INSTALL_DIR/runme.R</action> | 25 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos="http://cran.us.r-project.org")" >> $INSTALL_DIR/runme.R</action> |
| 20 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> | 26 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> |
| 21 <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> | 27 <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> |
| 22 </actions> | 28 </actions> |
| 23 </install> | 29 </install> |
| 24 <readme>Installs some basic bioc packages for the edgeR wrapper | 30 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs |
| 25 It's clunky but this is the only way I could get anything installed into the package_r3 R | 31 It's clunky but this is the most convenient way I could get anything installed into the package_r3 |
| 32 Note we use cran at fred hutch since no fastest mirror thingy | |
| 26 </readme> | 33 </readme> |
| 27 </package> | 34 </package> |
| 28 </tool_dependency> | 35 </tool_dependency> |