Mercurial > repos > bgruening > precommit_test

comparison tool_dependencies.xml @ 18:77d6b8ccc046 draft

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author bgruening
date Mon, 04 Nov 2013 04:04:03 -0500
parents 9ce50b97cd17
children 4b482f6136c2
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17:9ce50b97cd17 18:77d6b8ccc046
4 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" 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="trans_proteomic_pipeline" version="4.6.3"> 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 <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> 9 <action type="setup_perl_environment">
10 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
11 <package name="perl" version="5.18.1" />
12 </repository>
13 <!-- allow downloading and installing an Perl package from cpan.org-->
14
15 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
16 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
17 <package>XML::Parser</package>
18 -->
19 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
20
21
22 </action>
23 <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>
10 <!-- populate the environment variables from the dependend repos --> 24 <!-- populate the environment variables from the dependend repos -->
11 <action type="set_environment_for_install"> 25 <action type="set_environment_for_install">
12 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 26 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
13 <package name="libgd" version="2.1.0" /> 27 <package name="libgd" version="2.1.0" />
14 </repository> 28 </repository>
15 </action> 29 </action>
16 <action type="change_directory">./trans_proteomic_pipeline/src/</action> 30 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
17 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR' &gt; Makefile.config.incl</action> 31 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
18 <action type="make_install" /> 32 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc-1.8.27-8.debian.patched.tar.gz</action>
33
34 <action type="move_file">
35 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
36 <destination>./TPP-4.6.3/extern/htmldoc.tgz</destination>
37 </action>
38
39 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
40 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp' &gt; Makefile.config.incl</action>
41 <action type="shell_command">ls -l &gt; $INSTALL_DIR/foo.txt</action>
42 <action type="shell_command">cat Makefile.config.incl &gt; $INSTALL_DIR/foo2.txt</action>
43 <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB &amp;&amp; export PATH=$PERL_ROOT_DIR/bin/:$PATH &amp;&amp; make</action>
44 <action type="shell_command">make install</action>
19 <action type="set_environment"> 45 <action type="set_environment">
20 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
21 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> 47 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
22 </action> 48 </action>
23 </actions> 49 </actions>
30 56
31 PATH will be set. 57 PATH will be set.
32 TPP_ROOT_PATH will point to the root path of the installation. 58 TPP_ROOT_PATH will point to the root path of the installation.
33 </readme> 59 </readme>
34 </package> 60 </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.
56 </readme>
57 </package>
58 </tool_dependency> 61 </tool_dependency>