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comparison tool_dependencies.xml @ 19:4b482f6136c2 draft

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author bgruening
date Tue, 05 Nov 2013 12:32:08 -0500
parents 77d6b8ccc046
children 2ecce0ee7183
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18:77d6b8ccc046 19:4b482f6136c2
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="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="perl" version="5.18.1">
7 <repository changeset_revision="978287122b91" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package>
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="http://testtoolshed.g2.bx.psu.edu" />
11 </package>
6 <package name="trans_proteomic_pipeline" version="4.6.3"> 12 <package name="trans_proteomic_pipeline" version="4.6.3">
7 <install version="1.0"> 13 <install version="1.0">
8 <actions> 14 <actions>
9 <action type="setup_perl_environment"> 15 <action type="setup_perl_environment">
10 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 16 <repository changeset_revision="978287122b91" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
11 <package name="perl" version="5.18.1" /> 17 <package name="perl" version="5.18.1" />
12 </repository> 18 </repository>
13 <!-- allow downloading and installing an Perl package from cpan.org--> 19 <!-- allow downloading and installing an Perl package from cpan.org-->
14 20
15 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package> 21 <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. 22 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
17 <package>XML::Parser</package> 23 <package>XML::Parser</package>
18 --> 24 -->
19 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package> 25 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
20 26
21 27
22 </action> 28 </action>
29 <action type="change_directory">..</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> 30 <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>
24 <!-- populate the environment variables from the dependend repos --> 31 <!-- populate the environment variables from the dependend repos -->
25 <action type="set_environment_for_install"> 32 <action type="set_environment_for_install">
26 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 33 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
27 <package name="libgd" version="2.1.0" /> 34 <package name="libgd" version="2.1.0" />
28 </repository> 35 </repository>
29 </action> 36 </action>
30 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action> 37 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
31 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation --> 38 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
32 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc-1.8.27-8.debian.patched.tar.gz</action> 39 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action>
40 <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
41 <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
42 <!--
43 <action type="move_file" rename_to="htmldoc.tgz">
44 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
45 <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
46 </action>
47 -->
48 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
49 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
50 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
51 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
33 52
34 <action type="move_file"> 53 <!--
35 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source> 54 TPP is fails with a error due to an deprecated use of qw()
36 <destination>./TPP-4.6.3/extern/htmldoc.tgz</destination> 55 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
37 </action> 56 -->
57 <action type="shell_command">sed -i -e 's/ /(&amp;) /' ../perl/tpp_models.pl</action>
58 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
59 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
38 60
39 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action> 61 <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>
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/:$PATH &amp;&amp; make</action>
44 <action type="shell_command">make install</action> 62 <action type="shell_command">make install</action>
45 <action type="set_environment"> 63 <action type="set_environment">
46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 64 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
65 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
47 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> 66 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
48 </action> 67 </action>
49 </actions> 68 </actions>
50 </install> 69 </install>
51 <readme> 70 <readme>
52 Installs and complils the trans proteomic pipeline in version 4.6.3. 71 Installs and complils the trans proteomic pipeline in version 4.6.3.
53 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. 72 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
54 73
55 http://tools.proteomecenter.org/ 74 http://tools.proteomecenter.org/
56 75
76 Dependencies: e2fslibs-dev (e2fsprogs-devel)
77
57 PATH will be set. 78 PATH will be set.
58 TPP_ROOT_PATH will point to the root path of the installation. 79 TPP_ROOT_PATH will point to the root path of the installation.
59 </readme> 80 </readme>
60 </package> 81 </package>
61 </tool_dependency> 82 </tool_dependency>