Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 62:7b3d0a330e57 draft
Uploaded
| author | fubar |
|---|---|
| date | Mon, 10 Feb 2014 19:03:20 -0500 |
| parents | dfc1046c8806 |
| children | e4fc3bdf02cc |
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| 61:dfc1046c8806 | 62:7b3d0a330e57 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <!-- | |
| 4 Atlas will not compile for me - it thinks we have autoscaling on | |
| 5 so we need libopenblas-base installed on all nodes after commenting this and the set environment reference... | |
| 6 grrr | |
| 7 --> | |
| 8 <package name="atlas" version="3.11.11"> | |
| 9 <repository changeset_revision="02bc9f241131" name="package_atlas_3_11" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | |
| 10 </package> | |
| 11 | |
| 12 <package name="r302" version="3.0.2"> | 3 <package name="r302" version="3.0.2"> |
| 13 <repository changeset_revision="e5d9e2ca3ba6" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 4 <repository changeset_revision="e5d9e2ca3ba6" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 14 </package> | 5 </package> |
| 15 <package name="ghostscript" version="9.10"> | 6 <package name="ghostscript" version="9.10"> |
| 16 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 7 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 22 <install version="1.0"> | 13 <install version="1.0"> |
| 23 <actions> | 14 <actions> |
| 24 <action type="set_environment_for_install"> | 15 <action type="set_environment_for_install"> |
| 25 <repository changeset_revision="e5d9e2ca3ba6" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 16 <repository changeset_revision="e5d9e2ca3ba6" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 26 <package name="r302" version="3.0.2" /> | 17 <package name="r302" version="3.0.2" /> |
| 27 </repository> | |
| 28 <repository changeset_revision="02bc9f241131" name="package_atlas_3_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | |
| 29 <package name="atlas" version="3.11.11" /> | |
| 30 </repository> | 18 </repository> |
| 31 </action> | 19 </action> |
| 32 <action type="make_directory">$INSTALL_DIR</action> | 20 <action type="make_directory">$INSTALL_DIR</action> |
| 33 <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> |
| 34 <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> |