# HG changeset patch
# User iuc
# Date 1437157090 14400
# Node ID 2b778f0f7a0e20264aaac82bde3c6743968ca4a0
# Parent  6aff23e469060a7cad3f84b22f33f59b25e31175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

diff -r 6aff23e46906 -r 2b778f0f7a0e tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 19 15:03:23 2015 -0400
+++ b/tool_dependencies.xml	Fri Jul 17 14:18:10 2015 -0400
@@ -1,22 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="libgd" version="2.1.0">
-        <repository changeset_revision="3ec0c9e073da" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="perl" version="5.18.1">
-        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="expat" version="2.1.0">
         <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bzlib" version="1.0.6">
-        <repository changeset_revision="f744bc704064" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="libpng" version="1.2.5">
         <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="boost" version="1.55.0">
-        <repository changeset_revision="3c03e7c7f7bb" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="e2fsprogs" version="1.42.9">
         <repository changeset_revision="7bdf636806dd" name="package_e2fsprogs_1_42_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -25,7 +25,7 @@
         <install version="1.0">
             <actions>
                 <action type="setup_perl_environment">
-                    <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="perl" version="5.18.1" />
                     </repository>
                     <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
@@ -44,16 +44,16 @@
                 <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>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="3ec0c9e073da" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="libgd" version="2.1.0" />
                     </repository>
                     <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="libpng" version="1.2.5" />
                     </repository>
-                    <repository changeset_revision="f744bc704064" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="bzlib" version="1.0.6" />
                     </repository>
-                    <repository changeset_revision="3c03e7c7f7bb" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="boost" version="1.55.0" />
                     </repository>
                     <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
@@ -93,14 +93,14 @@
                 <!-- 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 $(BOOST_LIBDIR))" ""/' Makefile.incl</action>
-                <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action>
+                <action type="shell_command">sed -i.bak -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action>
+                <action type="shell_command">sed -i.bak -e 's/# Proteowizrd/endif/' Makefile.incl</action>
                 <!-- replace build-in expat library with the more recent toolshed one -->
-                <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action>
-                <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action>
+                <action type="shell_command">sed -i.bak -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action>
+                <action type="shell_command">sed -i.bak -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action>
 
-                <action type="shell_command">sed -i -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action>
-                <action type="shell_command">sed -i -e 's/# put common.*/endif/' Makefile.incl</action>
+                <action type="shell_command">sed -i.bak -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action>
+                <action type="shell_command">sed -i.bak -e 's/# put common.*/endif/' Makefile.incl</action>
 
                 <action type="shell_command">cat Makefile.incl &gt; /home/bag/makefile.incl.txt</action>
 
@@ -110,9 +110,9 @@
                     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">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>-->
+                <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
+                <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
                 <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
 
                 <action type="shell_command">make</action>