Mercurial > repos > morinlab > package_vardictjava_1_4_6

diff tool_dependencies.xml @ 0:53f0323d032c draft default tip

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/packages/package_vardictjava_1_4_6 commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:07:55 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 11 14:07:55 2016 -0400
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="vardictjava" version="1.4.6">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone https://github.com/AstraZeneca-NGS/VarDictJava.git vardictjava</action>
+                <action type="shell_command">git checkout tags/v1.4.6; git submodule update --init --recursive</action>
+                <action type="shell_command">bash ./gradlew clean installApp</action>
+                <action type="shell_command">chmod -R 775 .</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+            </actions>
+        </install>
+    </package>
+</tool_dependency>