Mercurial > repos > fubar > edger_test
comparison rgedgeR/tool_dependencies.xml @ 53:9cbc5a72fc3f draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 26 Jul 2013 23:46:52 -0400 |
| parents | 58bca54fa26b |
| children |
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| 52:58bca54fa26b | 53:9cbc5a72fc3f |
|---|---|
| 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="bf7e8f4749b4" 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> | 5 </package> |
| 6 <package name="biocbasics" version="2.12"> | 6 <package name="biocbasics" version="2.12"> |
| 7 <install version="1.0"> | 7 <install version="1.0"> |
| 8 <actions> | 8 <actions> |
| 9 <action type="set_environment_for_install"> | 9 <action type="set_environment_for_install"> |
| 10 <repository changeset_revision="bf7e8f4749b4" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 10 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 11 <package name="r3" version="3.0.1" /> | 11 <package name="r3" version="3.0.1" /> |
| 12 </repository> | 12 </repository> |
| 13 </action> | 13 </action> |
| 14 <action type="make_directory">$INSTALL_DIR</action> | 14 <action type="make_directory">$INSTALL_DIR</action> |
| 15 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> | 15 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> |
| 19 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" >> $INSTALL_DIR/runme.R</action> | 19 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" >> $INSTALL_DIR/runme.R</action> |
| 20 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> | 20 <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 $INSTALL_DIR/runme.R </action> | 21 <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> |
| 22 </actions> | 22 </actions> |
| 23 </install> | 23 </install> |
| 24 <readme>Installs some basic bioc packages for the edgeR wrapper | 24 <readme>Installs some basic bioc packages for the edgeR wrapper |
| 25 It's clunky but this is the only way I could get anything installed into the package_r3 R | 25 It's clunky but this is the only way I could get anything installed into the package_r3 R |
| 26 </readme> | 26 </readme> |
| 27 </package> | 27 </package> |
| 28 </tool_dependency> | 28 </tool_dependency> |