Mercurial > repos > iuc > package_tpp_4_6_3

comparison tool_dependencies.xml @ 3:679b2c6a6e19 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:17:32 -0400
parents aa519f1dda68
children
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2:aa519f1dda68 3:679b2c6a6e19
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="99a41bc40067" 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>
6 <package name="perl" version="5.18.1">
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>
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" />
11 </package>
12 <package name="bzlib" version="1.0.6">
13 <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 14 </package>
6 <package name="libpng" version="1.2.5"> 15 <package name="libpng" version="1.2.5">
7 <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" />
8 </package> 17 </package>
9 <package name="bzlib" version="1.0.6">
10 <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="perl" version="5.18.1">
13 <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="expat" version="2.1.0">
16 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="trans_proteomic_pipeline" version="4.6.3"> 18 <package name="trans_proteomic_pipeline" version="4.6.3">
19 <install version="1.0"> 19 <install version="1.0">
20 <actions> 20 <actions>
21 <!-- populate the environment variables from the dependent repos --> 21 <action type="setup_perl_environment">
22 <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
23 <package name="perl" version="5.18.1" />
24 </repository>
25 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
26 <package name="expat" version="2.1.0" />
27 </repository>
28 <!-- allow downloading and installing an Perl package from cpan.org-->
29 <package>http://cpan.metacpan.org/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
30 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
31 <package>XML::Parser</package>
32 -->
33 <package>http://cpan.metacpan.org/authors/id/L/LD/LDS/CGI.pm-3.49.tar.gz</package>
34 </action>
35 <action type="change_directory">..</action>
36 <action type="download_file">https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz</action>
37 <!-- populate the environment variables from the dependend repos -->
22 <action type="set_environment_for_install"> 38 <action type="set_environment_for_install">
23 <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 39 <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
24 <package name="libgd" version="2.1.0" /> 40 <package name="libgd" version="2.1.0" />
25 </repository> 41 </repository>
26 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 42 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
27 <package name="libpng" version="1.2.5" /> 43 <package name="libpng" version="1.2.5" />
28 </repository> 44 </repository>
29 <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 45 <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
30 <package name="bzlib" version="1.0.6" /> 46 <package name="bzlib" version="1.0.6" />
47 </repository>
48 <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
49 <package name="perl" version="5.18.1" />
31 </repository> 50 </repository>
32 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 51 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
33 <package name="expat" version="2.1.0" /> 52 <package name="expat" version="2.1.0" />
34 </repository> 53 </repository>
35 <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
36 <package name="perl" version="5.18.1" />
37 </repository>
38 </action> 54 </action>
39 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action> 55 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
40 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action> 56 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action> 57 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action>
42 <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action> 58 <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
59 <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
60 <!--
61 <action type="move_file" rename_to="htmldoc.tgz">
62 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
63 <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
64 </action>
65 -->
66 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
67 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
68 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
69 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
43 70
44 <!-- Change deprecated CGI endform to end_form --> 71 <!--
45 <action type="shell_command">sed -i.orig 's/endform/end_form/' TPP-4.6.3/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl</action> 72 TPP is fails with a error due to an deprecated use of qw()
73 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
74 -->
75 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>
76 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
77 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
78 <!--action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action-->
46 79
47 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action> 80 <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>
48 <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/" &gt; Makefile.config.incl</action> 81 <action type="shell_command">make install</action>
49 <action type="shell_command">echo "TPP_WEB=/tpp/" &gt;&gt; Makefile.config.incl</action>
50 <action type="shell_command">echo "XSLT_PROC=/usr/bin/xsltproc" &gt;&gt; Makefile.config.incl</action>
51 <action type="shell_command">echo "CGI_USER_DIR=$INSTALL_DIR/cgi-bin/" &gt;&gt; Makefile.config.incl</action>
52
53 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
54 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
55 <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
56
57 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
58
59 <action type="set_environment"> 82 <action type="set_environment">
60 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 83 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
84 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
61 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> 85 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
62 </action> 86 </action>
63
64 </actions> 87 </actions>
65 </install> 88 </install>
66 <readme> 89 <readme>
67 Installs and compiles the trans proteomic pipeline in version 4.6.3 90 Installs and complils the trans proteomic pipeline in version 4.6.3.
68 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. 91 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
69 92
70 http://tools.proteomecenter.org/ 93 http://tools.proteomecenter.org/
94
95 Dependencies: e2fslibs-dev (e2fsprogs-devel)
71 96
72 PATH will be set. 97 PATH will be set.
73 TPP_ROOT_PATH will point to the root path of the installation. 98 TPP_ROOT_PATH will point to the root path of the installation.
74 </readme> 99 </readme>
75 </package> 100 </package>