# HG changeset patch
# User bgruening
# Date 1395085543 14400
# Node ID f35b0eeda699d16fde732279e4d8a8c3a10ffded
# Parent  8fb6f74d7db61812f8f775913a7fe10388e53a0e
Uploaded

diff -r 8fb6f74d7db6 -r f35b0eeda699 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 16 16:27:11 2014 -0400
+++ b/tool_dependencies.xml	Mon Mar 17 15:45:43 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="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e89ba6f88ab2" 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" />
@@ -47,7 +47,7 @@
                     <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="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="e89ba6f88ab2" 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">
@@ -60,9 +60,11 @@
                 <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="make_directory">../build/</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 'OBJ_ARCH=../build' &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>
@@ -70,6 +72,8 @@
                 <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 'HTMLDOC_BIN=' &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>
@@ -78,7 +82,9 @@
                 <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>
+                <action type="shell_command">cat Makefile.config.incl &gt; /home/bag/blablabla.txt</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.
                 -->
@@ -88,6 +94,13 @@
                 <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>
 
+                <action type="shell_command">sed -i -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action>
+                <action type="shell_command">sed -i -e 's/# put common.*/endif/' Makefile.incl</action>
+
+                <action type="shell_command">cat Makefile.incl &gt; /home/bag/makefile.incl.txt</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