Mercurial > repos > iuc > package_tpp_4_7_0

comparison tool_dependencies.xml @ 1:2b778f0f7a0e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:18:10 -0400
parents 6aff23e46906
children
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0:6aff23e46906 1:2b778f0f7a0e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
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="3ec0c9e073da" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="bzlib" version="1.0.6"> 12 <package name="bzlib" version="1.0.6">
13 <repository changeset_revision="f744bc704064" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="libpng" version="1.2.5"> 15 <package name="libpng" version="1.2.5">
16 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="boost" version="1.55.0"> 18 <package name="boost" version="1.55.0">
19 <repository changeset_revision="3c03e7c7f7bb" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 19 <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
20 </package> 20 </package>
21 <package name="e2fsprogs" version="1.42.9"> 21 <package name="e2fsprogs" version="1.42.9">
22 <repository changeset_revision="7bdf636806dd" name="package_e2fsprogs_1_42_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 22 <repository changeset_revision="7bdf636806dd" name="package_e2fsprogs_1_42_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 28 <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.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="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 31 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
32 <package name="expat" version="2.1.0" /> 32 <package name="expat" version="2.1.0" />
33 </repository> 33 </repository>
42 </action> 42 </action>
43 <action type="change_directory">..</action> 43 <action type="change_directory">..</action>
44 <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> 44 <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>
45 <!-- populate the environment variables from the dependend repos --> 45 <!-- populate the environment variables from the dependend repos -->
46 <action type="set_environment_for_install"> 46 <action type="set_environment_for_install">
47 <repository changeset_revision="3ec0c9e073da" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 47 <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
48 <package name="libgd" version="2.1.0" /> 48 <package name="libgd" version="2.1.0" />
49 </repository> 49 </repository>
50 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 50 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
51 <package name="libpng" version="1.2.5" /> 51 <package name="libpng" version="1.2.5" />
52 </repository> 52 </repository>
53 <repository changeset_revision="f744bc704064" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 53 <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
54 <package name="bzlib" version="1.0.6" /> 54 <package name="bzlib" version="1.0.6" />
55 </repository> 55 </repository>
56 <repository changeset_revision="3c03e7c7f7bb" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 56 <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
57 <package name="boost" version="1.55.0" /> 57 <package name="boost" version="1.55.0" />
58 </repository> 58 </repository>
59 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 59 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
60 <package name="expat" version="2.1.0" /> 60 <package name="expat" version="2.1.0" />
61 </repository> 61 </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">