|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
2
|
3 <package name="libgd" version="2.1.0">
|
|
9
|
4 <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
5
|
5 </package>
|
|
|
6 <package name="libpng" version="1.2.5">
|
|
10
|
7 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
5
|
8 </package>
|
|
|
9 <package name="bzlib" version="1.0.6">
|
|
9
|
10 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
2
|
11 </package>
|
|
|
12 <package name="perl" version="5.18.1">
|
|
|
13 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
|
14 </package>
|
|
|
15 <package name="expat" version="2.1.0">
|
|
|
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>
|
|
|
18 <package name="trans_proteomic_pipeline" version="4.6.1">
|
|
|
19 <install version="1.0">
|
|
|
20 <actions>
|
|
10
|
21 <!-- populate the environment variables from the dependent repos -->
|
|
2
|
22 <action type="set_environment_for_install">
|
|
9
|
23 <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
2
|
24 <package name="libgd" version="2.1.0" />
|
|
|
25 </repository>
|
|
10
|
26 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
5
|
27 <package name="libpng" version="1.2.5" />
|
|
|
28 </repository>
|
|
9
|
29 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
5
|
30 <package name="bzlib" version="1.0.6" />
|
|
|
31 </repository>
|
|
2
|
32 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
|
33 <package name="expat" version="2.1.0" />
|
|
|
34 </repository>
|
|
|
35 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.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>
|
|
3
|
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>
|
|
4
|
41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.1.tgz</action>
|
|
3
|
42 <action type="shell_command">tar -zxf TPP-4.6.1.tgz</action>
|
|
|
43
|
|
|
44 <action type="change_directory">./TPP-4.6.1/trans_proteomic_pipeline/src/</action>
|
|
|
45 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action>
|
|
|
46 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action>
|
|
|
47 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action>
|
|
|
48
|
|
5
|
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/" > "Makefile.config.incl"</action>
|
|
|
50
|
|
|
51
|
|
|
52 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action>
|
|
|
53 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action>
|
|
3
|
54
|
|
|
55 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
|
|
|
56
|
|
10
|
57 <action type="set_environment">
|
|
|
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
|
|
|
59 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
|
|
|
60 </action>
|
|
|
61
|
|
2
|
62 </actions>
|
|
|
63 </install>
|
|
|
64 <readme>
|
|
6
|
65 Installs and compiles the trans proteomic pipeline in version 4.6.1
|
|
2
|
66 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
|
|
1
|
67
|
|
2
|
68 http://tools.proteomecenter.org/
|
|
|
69
|
|
|
70 PATH will be set.
|
|
|
71 TPP_ROOT_PATH will point to the root path of the installation.
|
|
|
72 </readme>
|
|
|
73 </package>
|
|
0
|
74 </tool_dependency>
|
