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comparison tool_dependencies.xml @ 17:9ce50b97cd17 draft

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author bgruening
date Sun, 03 Nov 2013 10:08:01 -0500
parents bd5da1454a9b
children 77d6b8ccc046
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16:bd5da1454a9b 17:9ce50b97cd17
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="perl" version="5.18.1"> 3 <package name="libgd" version="2.1.0">
4 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="bioperl" version="1.6.922"> 6 <package name="trans_proteomic_pipeline" version="4.6.3">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <!-- install perl --> 9 <action type="download_by_url">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>
10 <!--<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</action>-->
11 <!-- populate the environment variables from the dependend repos --> 10 <!-- populate the environment variables from the dependend repos -->
12 <action type="set_environment_for_install"> 11 <action type="set_environment_for_install">
13 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 12 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
14 <package name="perl" version="5.18.1" /> 13 <package name="libgd" version="2.1.0" />
15 </repository> 14 </repository>
16 </action> 15 </action>
17 16 <action type="change_directory">./trans_proteomic_pipeline/src/</action>
18 <action type="shell_command">cpanm --local-lib=$INSTALL_DIR XML::Parser</action> 17 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR' &gt; Makefile.config.incl</action>
19 <action type="shell_command">cpanm --local-lib=$INSTALL_DIR Bundle::BioPerl</action> 18 <action type="make_install" />
20
21
22 <action type="set_environment"> 19 <action type="set_environment">
23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 20 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
24 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> 21 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
25 <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR/lib</environment_variable>
26 </action> 22 </action>
27 </actions> 23 </actions>
28 </install> 24 </install>
29 <readme> 25 <readme>
30 Bundle::BioPerl 26 Installs and complils the trans proteomic pipeline in version 4.6.3.
27 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
28
29 http://tools.proteomecenter.org/
30
31 PATH will be set.
32 TPP_ROOT_PATH will point to the root path of the installation.
33 </readme>
34 </package>
35 <package name="tpp_perllibs" version="4.6.3">
36 <install version="1.0">
37 <actions>
38 <action type="setup_perl_environment">
39 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
40 <package name="perl" version="5.18.1" />
41 </repository>
42 <!-- allow downloading and installing an Perl package from cpan.org-->
43
44 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
45 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
46 <package>XML::Parser</package>
47 -->
48 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
49
50
51 </action>
52 </actions>
53 </install>
54 <readme>
55 TPP Perl dependencies.
31 </readme> 56 </readme>
32 </package> 57 </package>
33 </tool_dependency> 58 </tool_dependency>