changeset 72:cb32520e1e37

Uploaded

--- a/tool_dependencies.xml	Fri Nov 01 19:43:11 2013 -0400
+++ b/tool_dependencies.xml	Mon Nov 11 04:24:36 2013 -0500
@@ -1,35 +1,20 @@
-<?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">
+    <package name="CCAT" version="3.0">
         <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 type="download_by_url">http://cmb.gis.a-star.edu.sg/ChIPSeq/tools/CCAT3.0.tar.gz</action>
+                <action type="change_directory">src</action>
+                <action type="shell_command">./make</action>
+                <action type="move_file">
+                    <source>../bin/CCAT</source>
+                    <destination>$INSTALL_DIR/bin</destination>
                 </action>
-                <action type="change_directory">./trans_proteomic_pipeline/src/</action>
-                <action type="shell_command">echo 'TPP_ROOT=$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>
+        <readme>Downloading  and compiling CCAT. A Signal-Noise model for significance analysis of ChIP-seq with Negative Control.</readme>
     </package>
 </tool_dependency>