# HG changeset patch
# User bgruening
# Date 1395001631 14400
# Node ID 8fb6f74d7db61812f8f775913a7fe10388e53a0e
# Parent  b568a3db8e2c6c2f5046a82f05a40c84a5f579e9
Uploaded

diff -r b568a3db8e2c -r 8fb6f74d7db6 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Mar 15 06:25:04 2014 -0400
+++ b/tool_dependencies.xml	Sun Mar 16 16:27:11 2014 -0400
@@ -10,7 +10,7 @@
         <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" />
+        <repository changeset_revision="c8aecd67e0f5" 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" />
@@ -35,6 +35,7 @@
                         <package>XML::Parser</package>
                     -->
                    <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
+                   <!--<package>http://search.cpan.org/CPAN/authors/id/S/SK/SKIMO/FCGI-0.67.tar.gz</package>-->
                 </action>
                 <action type="change_directory">..</action>
                 <action type="download_file">http://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.7%20%28polar%20vortex%29%20rev%200/TPP_4.7.0-src.tgz</action>
@@ -46,46 +47,61 @@
                     <repository changeset_revision="821c27341c0e" 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="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="bzlib" version="1.0.6" />
                     </repository>
                     <repository changeset_revision="1d696f0a53b9" name="package_boost_1_53" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="boost" version="1.53.0" />
                     </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>
                 </action>
-                <action type="shell_command">tar xfz TPP-4.7.0.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">tar xfz TPP_4.7.0-src.tgz</action>
+
+                <action type="change_directory">./TPP-4.7.0/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 'BOOST_INCL=-I$BOOST_ROOT_DIR' &gt;&gt; Makefile.config.incl</action>
-                <action type="shell_command">echo 'BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/' &gt;&gt; Makefile.config.incl</action>
-                <action type="shell_command">echo 'BOOST_LIBSPEC=-gcc43-mt' &gt;&gt; Makefile.config.incl</action>
+                <!-- define some BOOST variables to link against the toolshed boost version -->
+                <action type="shell_command">echo "BOOST_DIR=$BOOST_ROOT_DIR" &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo "BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/" &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'BOOST_LIB_EXT=so' &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'BOOST_INCL=-isystem $(BOOST_DIR) -isystem $(BOOST_DIR)/.. -I$(SRC_ROOT).' &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'BOOST_LIBS=$(BOOST_LIBDIR)*' &gt;&gt; Makefile.config.incl</action>
+
                 <action type="shell_command">echo 'LINK=shared' &gt;&gt; Makefile.config.incl</action>
                 <action type="shell_command">echo 'LIBEXT=so' &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo "BZ2_LIB=$BZLIB_LIB_DIR/libbz2.a" &gt;&gt; Makefile.config.incl</action>
+
+                <action type="shell_command">echo "EXPAT_LIB=$EXPAT_ROOT_DIR/lib/libexpat.a" &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo "EXPAT_INCL=$EXPAT_ROOT_DIR/include/" &gt;&gt; Makefile.config.incl</action>
+
+                <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action>
+                <!-- do not use the build-in boost version 
+                    Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch.
+                -->
+                <action type="shell_command">sed -i -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action>
+                <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action>
+                <!-- replace build-in expat library with the more recent toolshed one -->
+                <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action>
+                <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.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">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">
+                    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/tpp/bin</environment_variable>
@@ -100,8 +116,6 @@
 
             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>