Mercurial > repos > iuc > package_tpp_4_7_0

comparison tool_dependencies.xml @ 7:f732cb0203cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author iuc
date Thu, 16 Jul 2015 14:01:40 -0400
parents e4d50b87c220
children ce629de7e06c
comparison
equal deleted inserted replaced
6:e4d50b87c220 7:f732cb0203cb
2 <tool_dependency> 2 <tool_dependency>
3 <package name="libgd" version="2.1.0"> 3 <package name="libgd" version="2.1.0">
4 <repository changeset_revision="88f469bfafbf" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="88f469bfafbf" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="perl" version="5.18.1"> 6 <package name="perl" version="5.18.1">
7 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="expat" version="2.1.0"> 9 <package name="expat" version="2.1.0">
10 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="bzlib" version="1.0.6"> 12 <package name="bzlib" version="1.0.6">
23 </package> 23 </package>
24 <package name="trans_proteomic_pipeline" version="4.7.0"> 24 <package name="trans_proteomic_pipeline" version="4.7.0">
25 <install version="1.0"> 25 <install version="1.0">
26 <actions> 26 <actions>
27 <action type="setup_perl_environment"> 27 <action type="setup_perl_environment">
28 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 28 <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
29 <package name="perl" version="5.18.1" /> 29 <package name="perl" version="5.18.1" />
30 </repository> 30 </repository>
31 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 31 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
32 <package name="expat" version="2.1.0" /> 32 <package name="expat" version="2.1.0" />
33 </repository> 33 </repository>
91 91
92 92
93 <!-- do not use the build-in boost version 93 <!-- do not use the build-in boost version
94 Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch. 94 Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch.
95 --> 95 -->
96 <action type="shell_command">sed -i -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action> 96 <action type="shell_command">sed -i.bak -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action>
97 <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action> 97 <action type="shell_command">sed -i.bak -e 's/# Proteowizrd/endif/' Makefile.incl</action>
98 <!-- replace build-in expat library with the more recent toolshed one --> 98 <!-- replace build-in expat library with the more recent toolshed one -->
99 <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action> 99 <action type="shell_command">sed -i.bak -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action>
100 <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action> 100 <action type="shell_command">sed -i.bak -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action>
101 101
102 <action type="shell_command">sed -i -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action> 102 <action type="shell_command">sed -i.bak -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action>
103 <action type="shell_command">sed -i -e 's/# put common.*/endif/' Makefile.incl</action> 103 <action type="shell_command">sed -i.bak -e 's/# put common.*/endif/' Makefile.incl</action>
104 104
105 <action type="shell_command">cat Makefile.incl &gt; /home/bag/makefile.incl.txt</action> 105 <action type="shell_command">cat Makefile.incl &gt; /home/bag/makefile.incl.txt</action>
106 106
107 107
108 108
109 <!-- 109 <!--
110 TPP is fails with a error due to an deprecated use of qw() 110 TPP is fails with a error due to an deprecated use of qw()
111 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html 111 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
112 --> 112 -->
113 <!--<action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>--> 113 <!--<action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>-->
114 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action> 114 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
115 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action> 115 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
116 <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action> 116 <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
117 117
118 <action type="shell_command">make</action> 118 <action type="shell_command">make</action>
119 <action type="shell_command">make install</action> 119 <action type="shell_command">make install</action>
120 <action type="set_environment"> 120 <action type="set_environment">