Mercurial > repos > yhoogstrate > edger_with_design_matrix
comparison tool_dependencies.xml @ 96:aef2ea94533b draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 73d87531bc80b0a4e688001cd5f8ab1df9526c08-dirty
| author | yhoogstrate |
|---|---|
| date | Wed, 27 May 2015 09:00:14 -0400 |
| parents | 86c3aaa205b5 |
| children | b26040bb6301 |
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| 95:9dac2146b98c | 96:aef2ea94533b |
|---|---|
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="R" version="3.0.3"> | 3 <package name="R" version="3.0.3"> |
| 4 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 4 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 5 </package> | 5 </package> |
| 6 | 6 |
| 7 <package name="biocLite_edgeR_limma" version="latest"> | 7 <package name="package_biocLite_edgeR_limma_latest" version="latest"> |
| 8 <install version="1.0"> | 8 <install version="1.0"> |
| 9 <actions> | 9 <actions> |
| 10 | |
| 10 <action type="set_environment_for_install"> | 11 <action type="set_environment_for_install"> |
| 11 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 12 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 12 <package name="R" version="3.0.3" /> | 13 <package name="R" version="3.0.3" /> |
| 13 </repository> | 14 </repository> |
| 14 | |
| 15 </action> | 15 </action> |
| 16 | |
| 16 <action type="make_directory">$INSTALL_DIR</action> | 17 <action type="make_directory">$INSTALL_DIR</action> |
| 17 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> | 18 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> |
| 18 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action> | 19 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action> |
| 19 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> | 20 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> |
| 20 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> | 21 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> |
| 26 <readme> | 27 <readme> |
| 27 Installs the latest bioc packages: edgeR & Limma | 28 Installs the latest bioc packages: edgeR & Limma |
| 28 </readme> | 29 </readme> |
| 29 </package> | 30 </package> |
| 30 | 31 |
| 31 <package name="design_matrix_creator" version="1.0.0"> | 32 <package name="package_design_matrix_creator_1_0_0" version="1.0.0"> |
| 32 <install version="1.0"> | 33 <install version="1.0"> |
| 33 <actions> | 34 <actions> |
| 34 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action> | 35 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action> |
| 35 <action type="chmod"> | 36 <action type="chmod"> |
| 36 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file> | 37 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file> |
| 41 </action> | 42 </action> |
| 42 </actions> | 43 </actions> |
| 43 </install> | 44 </install> |
| 44 </package> | 45 </package> |
| 45 | 46 |
| 46 <package name="edger_dge_table_to_bedgraph" version="1.0.0"> | 47 <package name="package_edger_dge_table_to_bedgraph_1_0_0" version="1.0.0"> |
| 47 <install version="1.0"> | 48 <install version="1.0"> |
| 48 <actions> | 49 <actions> |
| 49 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action> | 50 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action> |
| 50 <action type="chmod"> | 51 <action type="chmod"> |
| 51 <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file> | 52 <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file> |