changeset 17:9ce50b97cd17 draft

Uploaded

--- a/tool_dependencies.xml	Sat Nov 02 20:44:31 2013 -0400
+++ b/tool_dependencies.xml	Sun Nov 03 10:08:01 2013 -0500
@@ -1,33 +1,58 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="libgd" version="2.1.0">
+        <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="bioperl" version="1.6.922">
+    <package name="trans_proteomic_pipeline" version="4.6.3">
         <install version="1.0">
             <actions>
-                <!-- install perl -->
-                <!--<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</action>-->
+                <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="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="perl" version="5.18.1" />
+                    <repository changeset_revision="dcbab64c0429" 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="shell_command">cpanm --local-lib=$INSTALL_DIR XML::Parser</action>
-                <action type="shell_command">cpanm --local-lib=$INSTALL_DIR Bundle::BioPerl</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="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
-                    <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
-            Bundle::BioPerl
+            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>
+    <package name="tpp_perllibs" version="4.6.3">
+        <install version="1.0">
+            <actions>
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="091a97f8c585" 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>
+            </actions>
+        </install>
+        <readme>
+            TPP Perl dependencies.
         </readme>
     </package>
 </tool_dependency>