changeset 69:f6e879c9ce85

Uploaded

--- a/tool_dependencies.xml	Wed Oct 30 10:08:52 2013 -0400
+++ b/tool_dependencies.xml	Fri Nov 01 19:42:27 2013 -0400
@@ -1,23 +1,35 @@
-<?xml version="1.0"?>
-<tool_dependency>
-<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help -->
-    <package name="xtandem" version="12.10011">
-        <install version="12.10011">
-            <actions>
-                <action type="download_by_url">ftp://ftp.thegpm.org/projects/tandem/source/2011-12-01/tandem-linux-12-10-01-1.zip</action>
-                <!--<action type="shell_command">make clean</action>
-                <action type="shell_command">make</action>-->
-                <action type="move_directory_files">
-					<source_directory>tandem-linux-12-10-01-1</source_directory>
-					<destination_directory>$INSTALL_DIR/tandem-linux-12-10-01-1</destination_directory>
-				</action>
-                <action type="set_environment">
-                    <environment_variable name="XTANDEM_12_10_01_PATH" action="set_to">$INSTALL_DIR/tandem-linux-12-10-01-1</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Ensures XTandem is installed.
-        </readme>
-    </package>
-</tool_dependency>
\ No newline at end of file
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="libgd" version="2.1.0">
+        <repository changeset_revision="1efb934d4600" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.6.3">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz</action>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="1efb934d4600" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libgd" version="2.1.0" />
+                    </repository>
+                </action>
+                <action type="change_directory">./trans_proteomic_pipeline/src/</action>
+                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR' &gt; Makefile.config.incl</action>
+                <action type="make_install" />
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installs and complils the trans proteomic pipeline in version 4.6.3.
+            The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
+
+            http://tools.proteomecenter.org/
+
+            PATH will be set.
+            TPP_ROOT_PATH will point to the root path of the installation.
+        </readme>
+    </package>
+</tool_dependency>