Mercurial > repos > insilico-bob > ngchm_dependencies
comparison tool_dependencies.xml @ 4:d3d47c77ec79 draft
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author | insilico-bob |
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date | Fri, 06 Jan 2017 15:53:10 -0500 |
parents | 715e125409e2 |
children | 1abdad49a3ec |
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3:715e125409e2 | 4:d3d47c77ec79 |
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1 <?xml version="1.0"?> | 1 <tool_dependency > |
2 <tool_dependency> | 2 <!-- https://wiki.galaxyproject.org/ToolDependenciesTagSets --> |
3 <package name="ngchm" version="1.2"> | 3 <actions> |
4 <install version="1.0"> | 4 <action type="shell_command">echo 'starting tool dependency script'</action> |
5 <actions> | 5 <action type="change_directory">/shed_tools/toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm_dependencies/*/ngchm_dependencies/</action> |
6 <action type="shell_command">cd $GALAXY_ROOT_DIR</action> | 6 <action type="chmod"><file mode="755">./MDAHeatmap/*</file></action> |
7 <action type="shell_command">hg clone https://insilico-bob@toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm</action> | 7 <!--##### Place MDA software in Tools and Visualization directories ##### --> |
8 <action type="shell_command">mkdir -p -m 777 $GALAXY_ROOT_DIR/test-data/MDAheatmap</action> | 8 <action type="shell_command">echo 'Place MD Anderson test input and output files in ~/test-data directory'</action> |
9 <action type="move_directory_files"> | 9 <action type="shell_command">mkdir $GALAXY_ROOT/config/plugins/visualizations/mda_heatmap_viz/</action> |
10 <source_directory>./TestFiles</source_directory> | 10 <action type="move_directory_files"><source_directory>./MDAHeatmap/</source_directory><destination_directory>$GALAXY_ROOT/config/plugins/visualizations/mda_heatmap_viz/</destination_directory></action> |
11 <destination_directory>$GALAXY_ROOT_DIR/test-data/MDAheatmap</destination_directory> | 11 <!-- ##### Place MD Anderson test input and output files in ~/test-data directory ##### --> |
12 </action> | 12 <action type="shell_command">echo 'Place MD Anderson software in test data directories'</action> |
13 <action type="shell_command">mkdir -p -m 777 $GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/</action> | 13 <action type="move_directory_files"><source_directory>./TestFiles/</source_directory><destination_directory>$GALAXY_ROOT/test-data/</destination_directory></action> |
14 <action type="move_directory_files"> | 14 </actions> |
15 <source_directory>./MDAheatmap/</source_directory> | |
16 <destination_directory>$GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/</destination_directory> | |
17 </action> | |
18 <action type="shell_command">cd $GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/templates</action> | |
19 <action type="shell_command">make</action> | |
20 </actions> | |
21 </install> | |
22 <readme>Completed adding MDAnderson ngchm tool to Galaxy</readme> | |
23 </package> | |
24 </tool_dependency> | 15 </tool_dependency> |