Mercurial > repos > iracooke > package_tpp_4_6_1

comparison tool_dependencies.xml @ 5:bfcfbba3403e

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Uploaded
author iracooke
date Wed, 06 Nov 2013 00:52:39 -0500
parents c4c50fbac9d9
children c0e73546cd42
comparison
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4:c4c50fbac9d9 5:bfcfbba3403e
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="b17bbb1a41da" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="016ad1de8f18" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="libpng" version="1.2.5">
7 <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="bzlib" version="1.0.6">
10 <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package> 11 </package>
6 <package name="perl" version="5.18.1"> 12 <package name="perl" version="5.18.1">
7 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package> 14 </package>
9 <package name="expat" version="2.1.0"> 15 <package name="expat" version="2.1.0">
12 <package name="trans_proteomic_pipeline" version="4.6.1"> 18 <package name="trans_proteomic_pipeline" version="4.6.1">
13 <install version="1.0"> 19 <install version="1.0">
14 <actions> 20 <actions>
15 <!-- populate the environment variables from the dependend repos --> 21 <!-- populate the environment variables from the dependend repos -->
16 <action type="set_environment_for_install"> 22 <action type="set_environment_for_install">
17 <repository changeset_revision="b17bbb1a41da" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 23 <repository changeset_revision="016ad1de8f18" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
18 <package name="libgd" version="2.1.0" /> 24 <package name="libgd" version="2.1.0" />
25 </repository>
26 <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
27 <package name="libpng" version="1.2.5" />
28 </repository>
29 <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
30 <package name="bzlib" version="1.0.6" />
19 </repository> 31 </repository>
20 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 32 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
21 <package name="expat" version="2.1.0" /> 33 <package name="expat" version="2.1.0" />
22 </repository> 34 </repository>
23 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 35 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
32 <action type="change_directory">./TPP-4.6.1/trans_proteomic_pipeline/src/</action> 44 <action type="change_directory">./TPP-4.6.1/trans_proteomic_pipeline/src/</action>
33 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action> 45 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
34 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action> 46 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
35 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action> 47 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
36 48
37 <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" &gt; "TPP-$tpp_version/trans_proteomic_pipeline/src/Makefile.config.incl"</action> 49 <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" &gt; "Makefile.config.incl"</action>
50
51
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>
38 54
39 <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>
40 56
41 </actions> 57 </actions>
42 </install> 58 </install>