# HG changeset patch
# User bgruening
# Date 1402319769 14400
# Node ID 2460a279dee748ff906d1a12585d9ed5e2ee4cce
# Parent  21c3adbcbd0cffe3f0d52d90683d6bb3ba08ade5
Uploaded

diff -r 21c3adbcbd0c -r 2460a279dee7 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 12 22:34:10 2014 -0400
+++ b/tool_dependencies.xml	Mon Jun 09 09:16:09 2014 -0400
@@ -1,73 +1,99 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <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" />
+        <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://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 name="perl" version="5.18.1">
+        <repository changeset_revision="e89824189ec6" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://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="https://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" />
+        <repository changeset_revision="2dec91192fc7" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://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 name="libpng" version="1.2.5">
+        <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="trans_proteomic_pipeline" version="4.6.3">
         <install version="1.0">
             <actions>
-                <!-- populate the environment variables from the dependent repos -->
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="e89824189ec6" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://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 -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="libgd" version="2.1.0" />
                     </repository>
-                    <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="libpng" version="1.2.5" />
                     </repository>
-                    <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="2dec91192fc7" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="bzlib" version="1.0.6" />
                     </repository>
-                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="expat" version="2.1.0" />
-                    </repository>
-                    <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="e89824189ec6" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="perl" version="5.18.1" />
                     </repository>
+                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="expat" version="2.1.0" />
+                    </repository>
                 </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="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>
 
-                <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>
-
-
+                <!--
+                    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/qw(.*) /(&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">echo '' &gt; ../perl/tpp_models.pl</action>
 
-                <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
-
+                <action type="shell_command">export PERL5LIB=$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>
-            Installs and compiles the trans proteomic pipeline in version 4.6.3
+            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>