# HG changeset patch
# User iracooke
# Date 1394678050 14400
# Node ID 21c3adbcbd0cffe3f0d52d90683d6bb3ba08ade5
# Parent  be9d0ad8bea508535745c5f375df009e0a67f0f5
Uploaded

diff -r be9d0ad8bea5 -r 21c3adbcbd0c tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 12 22:25:20 2014 -0400
+++ b/tool_dependencies.xml	Wed Mar 12 22:34:10 2014 -0400
@@ -3,39 +3,22 @@
     <package name="libgd" version="2.1.0">
         <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="libpng" version="1.2.5">
+        <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bzlib" version="1.0.6">
+        <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" 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="d5188682d08e" 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="821c27341c0e" 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="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>
-                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="expat" version="2.1.0" />
-                    </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 -->
+                <!-- populate the environment variables from the dependent repos -->
                 <action type="set_environment_for_install">
                     <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="libgd" version="2.1.0" />
@@ -53,48 +36,38 @@
                         <package name="perl" version="5.18.1" />
                     </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="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action>
+                <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action>
+                <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action>
+                <action type="shell_command">tar -zxf TPP-4.6.3.tgz</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
-                -->
-                <!-- Most of these perl scripts are for Petunia so instead of patching just make them blank.  This has the added benefit of speeding things up and reducing the number of unwanted generated files -->
-                <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
+                <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" &gt; "Makefile.config.incl"</action>
+
+
                 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
-                <action type="shell_command">echo '' &gt; ../perl/exporTPP.pl</action>
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
+                <action type="shell_command">echo '' &gt; ../perl/tpp_models.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="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
+
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$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.
+            Installs and compiles 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>