# HG changeset patch
# User bgruening
# Date 1383555843 18000
# Node ID 77d6b8ccc0467312563ee0a67af3d28dde580ad8
# Parent  9ce50b97cd17f246a5d199282fe5224b0faee659
Uploaded

diff -r 9ce50b97cd17 -r 77d6b8ccc046 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Nov 03 10:08:01 2013 -0500
+++ b/tool_dependencies.xml	Mon Nov 04 04:04:03 2013 -0500
@@ -6,16 +6,42 @@
     <package name="trans_proteomic_pipeline" version="4.6.3">
         <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>
+                <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>
+                <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="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="change_directory">./trans_proteomic_pipeline/src/</action>
-                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR' &gt; Makefile.config.incl</action>
-                <action type="make_install" />
+                <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
+                <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
+                <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc-1.8.27-8.debian.patched.tar.gz</action>
+
+                <action type="move_file">
+                    <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
+                    <destination>./TPP-4.6.3/extern/htmldoc.tgz</destination>
+                </action>
+
+                <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
+                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp' &gt; Makefile.config.incl</action>
+                <action type="shell_command">ls -l &gt; $INSTALL_DIR/foo.txt</action>
+                <action type="shell_command">cat Makefile.config.incl &gt; $INSTALL_DIR/foo2.txt</action>
+                <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB &amp;&amp; export PATH=$PERL_ROOT_DIR/bin/:$PATH &amp;&amp; make</action>
+                <action type="shell_command">make install</action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                     <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
@@ -32,27 +58,4 @@
             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>