Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 96:e7d02e6b253c draft
Uploaded
| author | fubar |
|---|---|
| date | Sun, 02 Mar 2014 23:01:19 -0500 |
| parents | 8c96a2d95436 |
| children | 395197c30bf7 |
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| 95:8c96a2d95436 | 96:e7d02e6b253c |
|---|---|
| 7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 8 </package> | 8 </package> |
| 9 <package name="r303" version="3.0.3"> | 9 <package name="r303" version="3.0.3"> |
| 10 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 10 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 11 </package> | 11 </package> |
| 12 <set_environment version="1.0"> | |
| 13 <environment_variable action="set_to" name="RUNME_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> | |
| 14 </set_environment> | |
| 12 <package name="biocbasics" version="2.14"> | 15 <package name="biocbasics" version="2.14"> |
| 13 <install version="1.0"> | 16 <install version="1.0"> |
| 14 <actions> | 17 <actions> |
| 15 <action type="set_environment_for_install"> | 18 <action type="set_environment_for_install"> |
| 16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 19 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 17 <package name="r303" version="3.0.3" /> | 20 <package name="r303" version="3.0.3" /> |
| 18 </repository> | 21 </repository> |
| 19 </action> | 22 </action> |
| 20 <action type="make_directory">$INSTALL_DIR</action> | 23 <action type="make_directory">$INSTALL_DIR</action> |
| 21 <action type="shell_command">echo `ls -l`</action> | 24 <action type="shell_command">ls -l</action> |
| 22 | 25 <action type="shell_command">export PATH=$PATH && R CMD BATCH $RUNME_PATH/runme.R </action> |
| 23 <action type="shell_command">export PATH=$PATH && R CMD BATCH ./runme.R </action> | |
| 24 </actions> | 26 </actions> |
| 25 </install> | 27 </install> |
| 26 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs | 28 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs |
| 27 It's clunky but this is the most convenient way I could get anything installed into the package_r3 | 29 It's clunky but this is the most convenient way I could get anything installed into the package_r3 |
| 28 Note we use cran at fred hutch since no fastest mirror thingy | 30 Note we use cran at fred hutch since no fastest mirror thingy |