Mercurial > repos > iuc > package_openms_2_0

comparison tool_dependencies.xml @ 2:a3a898fdb393 draft

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author iuc
date Mon, 20 Apr 2015 11:09:24 -0400
parents 0a40bd585cd7
children 1a16c401c5a4
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1:0a40bd585cd7 2:a3a898fdb393
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <!-- ToDo can we get it easily without svn? Is this included in the final tarball? -->
3 <!-- svn checkout http://svn.code.sf.net/p/open-ms/code/THIRDPARTY/SEARCHENGINES/Linux/64bit/ _searchengines -->
4 <tool_dependency> 2 <tool_dependency>
5 <package name="openms" version="2.0"> 3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="psort" version="3.0.3">
6 <install version="1.0"> 7 <install version="1.0">
7 <actions_group> 8 <actions>
8 <actions architecture="x86_64" os="linux"> 9 <action type="download_by_url">http://www.psort.org/download/libpsortb-1.0.tar.gz</action>
9 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/openms/openms-2.0-Linux-x86_64.tar.gz</action> 10 <action type="autoconf" />
10 <action type="shell_command">rm openms-2.0-Linux-x86_64.tar.gz</action>
11 <action type="move_directory_files">
12 <source_directory>.</source_directory>
13 <destination_directory>$INSTALL_DIR</destination_directory>
14 </action>
15 <action type="set_environment">
16 <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
17 <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
19 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
20 </action>
21 </actions>
22 <actions architecture="x86_64" os="darwin">
23 <action type="download_by_url">https://github.com/OpenMS/OpenMS/archive/develop.tar.gz</action>
24 <action type="download_by_url">https://github.com/OpenMS/contrib/archive/master.tar.gz</action>
25 <action type="shell_command">mv contrib-master ../contrib</action>
26 <package name="libtool" version="2.4">
27 <repository name="package_libtool_2_4" owner="iuc" prior_installation_required="True" />
28 </package>
29 <package name="Qt" version="4.8">
30 <repository name="package_qt_4_8" owner="iuc" prior_installation_required="True" />
31 </package>
32 <package name="zlib" version="1.2.8">
33 <repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" />
34 </package>
35 <package name="bzlib" version="1.0.6">
36 <repository name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" />
37 </package>
38 <action type="set_environment_for_install">
39 <repository name="package_libtool_2_4" owner="iuc">
40 <package name="libtool" version="2.4" />
41 </repository>
42 <repository name="package_qt_4_8" owner="iuc">
43 <package name="Qt" version="4.8" />
44 </repository>
45 <repository name="package_zlib_1_2_8" owner="iuc">
46 <package name="zlib" version="1.2.8" />
47 </repository>
48 <repository name="package_bzlib_1_0" owner="iuc">
49 <package name="bzlib" version="1.0.6" />
50 </repository>
51 </action>
52 <action type="change_directory">../contrib</action>
53 <action type="shell_command">cmake . -DBUILD_TYPE=SEQAN</action>
54 <action type="shell_command">cmake . -DBUILD_TYPE=LIBSVM</action>
55 <action type="shell_command">cmake . -DBUILD_TYPE=XERCESC</action>
56 <action type="shell_command">cmake . -DBUILD_TYPE=GSL</action>
57 <action type="shell_command">cmake . -DBUILD_TYPE=BOOST -DNUMBER_OF_JOBS=4</action>
58 <action type="shell_command">cmake . -DBUILD_TYPE=COINOR</action>
59 <action type="shell_command">cmake . -DBUILD_TYPE=BZIP2</action>
60 <action type="shell_command">cmake . -DBUILD_TYPE=GLPK</action>
61 <action type="shell_command">cmake . -DBUILD_TYPE=EIGEN</action>
62 <action type="shell_command">cmake . -DBUILD_TYPE=WILDMAGIC</action>
63 11
64 <action type="change_directory">..</action> 12 <action type="download_by_url">ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/pft2.3.5.d.tar.gz</action>
65 <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF</action> 13 <action type="shell_command">make</action>
66 <action type="shell_command">make OpenMS TOPP UTILS</action> 14 <action type="move_directory_files">
67 <action type="shell_command">make install</action> 15 <source_directory>.</source_directory>
68 <action type="set_environment"> 16 <destination_directory>$INSTALL_DIR/pft</destination_directory>
69 <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable> 17 </action>
70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 18
71 <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable> 19 <action type="set_environment">
72 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> 20 <environment_variable action="set_to" name="LIBPSORTB_ROOT_PATH">$INSTALL_DIR</environment_variable>
73 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[QT_ROOT_DIR]/lib/</environment_variable> 21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
74 </action> 22 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/pft</environment_variable>
75 </actions> 23 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
76 </actions_group> 24 </action>
25
26 <action type="setup_perl_environment">
27 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
28 <package name="perl" version="5.18.1" />
29 </repository>
30 <!-- allow downloading and installing an Perl package from cpan.org-->
31 <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
32 <package>http://www.psort.org/download/bio-tools-psort-all.3.0.3.tar.gz</package>
33 </action>
34 </actions>
77 </install> 35 </install>
78 <readme> 36 <readme>
79 This package downloads and installs OpenMS. 37 http://www.psort.org/downloads/index.html
80 http://open-ms.sourceforge.net/
81 </readme> 38 </readme>
82 </package> 39 </package>
83 </tool_dependency> 40 </tool_dependency>