Mercurial > repos > insilico-bob > ngchm_dependencies

changeset 4:d3d47c77ec79 draft

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Uploaded
author insilico-bob
date Fri, 06 Jan 2017 15:53:10 -0500
parents 715e125409e2
children 1abdad49a3ec
files tool_dependencies.xml
diffstat 1 files changed, 14 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Dec 30 12:44:38 2016 -0500
+++ b/tool_dependencies.xml	Fri Jan 06 15:53:10 2017 -0500
@@ -1,24 +1,15 @@
-<?xml version="1.0"?>
-<tool_dependency>
- <package name="ngchm" version="1.2">
-    <install version="1.0">
-    <actions>
-        <action type="shell_command">cd $GALAXY_ROOT_DIR</action>
-        <action type="shell_command">hg clone https://insilico-bob@toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm</action>
-        <action type="shell_command">mkdir -p -m 777 $GALAXY_ROOT_DIR/test-data/MDAheatmap</action>
-        <action type="move_directory_files">
-           <source_directory>./TestFiles</source_directory>
-            <destination_directory>$GALAXY_ROOT_DIR/test-data/MDAheatmap</destination_directory>
-        </action>
-        <action type="shell_command">mkdir -p -m 777 $GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/</action>
-        <action type="move_directory_files">
-           <source_directory>./MDAheatmap/</source_directory>
-           <destination_directory>$GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/</destination_directory>
-        </action>
-        <action type="shell_command">cd $GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/templates</action>
-        <action type="shell_command">make</action>
-     </actions>
-   </install>
-   <readme>Completed adding MDAnderson ngchm tool to Galaxy</readme>
- </package>
+<tool_dependency >
+<!--  https://wiki.galaxyproject.org/ToolDependenciesTagSets -->
+      	<actions>
+      		<action type="shell_command">echo 'starting tool dependency script'</action>
+      		<action type="change_directory">/shed_tools/toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm_dependencies/*/ngchm_dependencies/</action>        		
+      		<action type="chmod"><file mode="755">./MDAHeatmap/*</file></action>
+<!--##### Place MDA software in Tools and Visualization directories #####   -->
+      		<action type="shell_command">echo 'Place MD Anderson test input and output files in ~/test-data directory'</action>
+      		<action type="shell_command">mkdir $GALAXY_ROOT/config/plugins/visualizations/mda_heatmap_viz/</action>
+      		<action type="move_directory_files"><source_directory>./MDAHeatmap/</source_directory><destination_directory>$GALAXY_ROOT/config/plugins/visualizations/mda_heatmap_viz/</destination_directory></action>
+<!-- ##### Place MD Anderson test input and output files in ~/test-data directory #####   -->
+      		<action type="shell_command">echo 'Place MD Anderson software in test data directories'</action>
+      		<action type="move_directory_files"><source_directory>./TestFiles/</source_directory><destination_directory>$GALAXY_ROOT/test-data/</destination_directory></action>
+      	</actions>
 </tool_dependency>