Mercurial > repos > iracooke > package_tpp_4_6_1

comparison tool_dependencies.xml @ 10:b856e62d76cf draft default tip

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author iracooke
date Mon, 03 Mar 2014 00:00:53 -0500
parents 9e12820b140d
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9:9e12820b140d 10:b856e62d76cf
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="2a074c7b442e" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="2a074c7b442e" 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="libpng" version="1.2.5"> 6 <package name="libpng" version="1.2.5">
7 <repository changeset_revision="d7f6d1ad51e2" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="bzlib" version="1.0.6"> 9 <package name="bzlib" version="1.0.6">
10 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="perl" version="5.18.1"> 12 <package name="perl" version="5.18.1">
16 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="trans_proteomic_pipeline" version="4.6.1"> 18 <package name="trans_proteomic_pipeline" version="4.6.1">
19 <install version="1.0"> 19 <install version="1.0">
20 <actions> 20 <actions>
21 <!-- populate the environment variables from the dependend repos --> 21 <!-- populate the environment variables from the dependent repos -->
22 <action type="set_environment_for_install"> 22 <action type="set_environment_for_install">
23 <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 23 <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
24 <package name="libgd" version="2.1.0" /> 24 <package name="libgd" version="2.1.0" />
25 </repository> 25 </repository>
26 <repository changeset_revision="d7f6d1ad51e2" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 26 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
27 <package name="libpng" version="1.2.5" /> 27 <package name="libpng" version="1.2.5" />
28 </repository> 28 </repository>
29 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 29 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
30 <package name="bzlib" version="1.0.6" /> 30 <package name="bzlib" version="1.0.6" />
31 </repository> 31 </repository>
52 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action> 52 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
53 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action> 53 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
54 54
55 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action> 55 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
56 56
57 <action type="set_environment">
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
59 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
60 </action>
61
57 </actions> 62 </actions>
58 </install> 63 </install>
59 <readme> 64 <readme>
60 Installs and compiles the trans proteomic pipeline in version 4.6.1 65 Installs and compiles the trans proteomic pipeline in version 4.6.1
61 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. 66 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.