Mercurial > repos > iuc > package_tpp_4_6_3

comparison tool_dependencies.xml @ 0:aad4e1a162c5

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author iuc
date Thu, 05 Jun 2014 19:27:54 -0400
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children 0bce36ee6bf2
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-1:000000000000 0:aad4e1a162c5
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="libgd" version="2.1.0">
4 <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="libpng" version="1.2.5">
7 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="bzlib" version="1.0.6">
10 <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="perl" version="5.18.1">
13 <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="expat" version="2.1.0">
16 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="trans_proteomic_pipeline" version="4.6.3">
19 <install version="1.0">
20 <actions>
21 <!-- populate the environment variables from the dependent repos -->
22 <action type="set_environment_for_install">
23 <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
24 <package name="libgd" version="2.1.0" />
25 </repository>
26 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
27 <package name="libpng" version="1.2.5" />
28 </repository>
29 <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
30 <package name="bzlib" version="1.0.6" />
31 </repository>
32 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
33 <package name="expat" version="2.1.0" />
34 </repository>
35 <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
36 <package name="perl" version="5.18.1" />
37 </repository>
38 </action>
39 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action>
40 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action>
41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action>
42 <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action>
43
44 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
45 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
46 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
47 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
48
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>
54 <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
55
56 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
57
58 <action type="set_environment">
59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
60 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
61 </action>
62
63 </actions>
64 </install>
65 <readme>
66 Installs and compiles the trans proteomic pipeline in version 4.6.3
67 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
68
69 http://tools.proteomecenter.org/
70
71 PATH will be set.
72 TPP_ROOT_PATH will point to the root path of the installation.
73 </readme>
74 </package>
75 </tool_dependency>