Mercurial > repos > yhoogstrate > edger_with_design_matrix
comparison tool_dependencies.xml @ 66:c8f607e8bd7b draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 30 Sep 2014 09:08:16 -0400 |
| parents | 8a4febbc60b7 |
| children | 718bb1dd0b8a |
comparison
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| 65:125c976723ad | 66:c8f607e8bd7b |
|---|---|
| 5 <package name="package_r3_withx" version="3.0.1"> | 5 <package name="package_r3_withx" version="3.0.1"> |
| 6 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 6 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 7 </package> | 7 </package> |
| 8 --> | 8 --> |
| 9 | 9 |
| 10 <!-- the following repo does NOT even install due to gfortran shared libs: | |
| 10 <package name="R" version="3.1.0"> | 11 <package name="R" version="3.1.0"> |
| 11 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 12 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 13 </package> | |
| 14 --> | |
| 15 | |
| 16 <package name="R" version="3.0.3"> | |
| 17 <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | |
| 12 </package> | 18 </package> |
| 13 | 19 |
| 14 <package name="package_biocLite_edgeR_limma" version="latest"> | 20 <package name="package_biocLite_edgeR_limma" version="latest"> |
| 15 <install version="1.0"> | 21 <install version="1.0"> |
| 16 <actions> | 22 <actions> |
| 18 <!-- the following repo does NOT work out of the box: | 24 <!-- the following repo does NOT work out of the box: |
| 19 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 25 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 20 <package name="package_r3_withx" version="3.0.1" /> | 26 <package name="package_r3_withx" version="3.0.1" /> |
| 21 </repository> | 27 </repository> |
| 22 --> | 28 --> |
| 29 <!-- the following repo does NOT even install due to gfortran shared libs: | |
| 23 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 30 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 24 <package name="R" version="3.1.0" /> | 31 <package name="R" version="3.1.0" /> |
| 25 </repository> | 32 </repository> |
| 33 --> | |
| 34 | |
| 35 <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | |
| 36 <package name="R" version="3.0.3" /> | |
| 37 </repository> | |
| 38 | |
| 26 </action> | 39 </action> |
| 27 <action type="make_directory">$INSTALL_DIR</action> | 40 <action type="make_directory">$INSTALL_DIR</action> |
| 28 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> | 41 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> |
| 29 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action> | 42 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action> |
| 30 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> | 43 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> |
| 33 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> | 46 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> |
| 34 <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> | 47 <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> |
| 35 </actions> | 48 </actions> |
| 36 </install> | 49 </install> |
| 37 <readme> | 50 <readme> |
| 38 Installs the latest bioc packages edgeR & Limma | 51 Installs the latest bioc packages: edgeR & Limma |
| 39 </readme> | 52 </readme> |
| 40 </package> | 53 </package> |
| 41 | 54 |
| 42 </tool_dependency> | 55 </tool_dependency> |