diff tool_dependencies.xml @ 1:a34ce2b18877 draft

Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie

--- a/tool_dependencies.xml	Wed Mar 20 09:17:14 2013 -0400
+++ b/tool_dependencies.xml	Fri Aug 30 10:56:26 2013 -0500
@@ -1,21 +1,13 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="trinityrnaseq" version="2013-02-25">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/trinityrnaseq/files/trinityrnaseq_r2013-02-25.tgz</action>
-                <action type="shell_command">make</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
+    <package name="trinityrnaseq" version="2013_08_14">
+        <repository changeset_revision="df23c0ef83a6" name="package_trinityrnaseq_2013_08_14" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="1.0.0">
+        <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>