# HG changeset patch
# User bgruening
# Date 1384432523 18000
# Node ID 6850407885a010e286dd38e66ff77a990c5bbc8a
# Parent  cb32520e1e375bc952a66702f4b3b7bb8ade7b85
Uploaded

diff -r cb32520e1e37 -r 6850407885a0 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 11 04:24:36 2013 -0500
+++ b/tool_dependencies.xml	Thu Nov 14 07:35:23 2013 -0500
@@ -1,20 +1,92 @@
+<?xml version="1.0"?>
 <tool_dependency>
-    <package name="CCAT" version="3.0">
+    <package name="libgd" version="2.1.0">
+        <repository changeset_revision="55e3d764c6c2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="expat" version="2.1.0">
+        <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bzlib" version="1.0.6">
+        <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libpng" version="1.2.5">
+        <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" 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">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 type="setup_perl_environment">
+                    <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                    <!-- allow downloading and installing an Perl package from cpan.org-->
+                   
+                    <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
+                    <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
+                        <package>XML::Parser</package>
+                    -->
+                   <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
+                </action>
+                <action type="change_directory">..</action>
+                <action type="download_file">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="55e3d764c6c2" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libgd" version="2.1.0" />
+                    </repository>
+                    <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.2.5" />
+                    </repository>
+                    <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="bzlib" version="1.0.6" />
+                    </repository>
                 </action>
+                <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
+                <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
+                <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action>
+                <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
+                <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
+                <!--
+                <action type="move_file" rename_to="htmldoc.tgz">
+                    <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
+                    <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
+                </action>
+                -->
+                <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
+                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
 
+                <!--
+                    TPP is fails with a error due to an deprecated use of qw()
+                    See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
+                -->
+                <action type="shell_command">sed -i -e 's/  /(&amp;) /' ../perl/tpp_models.pl</action>
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
+
+                <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB &amp;&amp; export PATH=$PERL_ROOT_DIR/bin/:$PATH &amp;&amp; export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB &amp;&amp; make</action>
+                <action type="shell_command">make install</action>
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
+                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>Downloading  and compiling CCAT. A Signal-Noise model for significance analysis of ChIP-seq with Negative Control.</readme>
+        <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/
+
+            Dependencies: e2fslibs-dev (e2fsprogs-devel)
+
+            PATH will be set.
+            TPP_ROOT_PATH will point to the root path of the installation.
+        </readme>
     </package>
 </tool_dependency>