Mercurial > repos > nml > package_python_3_4_hivtrace_0_1_4

comparison tool_dependencies.xml @ 0:38541eaf0d20 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
author nml
date Thu, 07 Jul 2016 09:58:46 -0400
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-1:000000000000 0:38541eaf0d20
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="python" version="3.4">
4 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="cmake" version="3.2.3">
7 <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="hyphy" version="2.2.6">
10 <repository changeset_revision="6e10967fdc7a" name="package_python_3_4_hyphy_2_2_6" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="pysam" version="0.8.3">
13 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="numpy" version="1.10.1">
16 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="biopython" version="1.66">
19 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
20 </package>
21 <package name="bioext" version="0.17.3">
22 <repository changeset_revision="d71e21675123" name="package_python_3_4_bioext_0_17_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
23 </package>
24 <package name="hppy" version="0.9.6">
25 <repository changeset_revision="ded93000c5da" name="package_python_3_4_hppy_0_9_6" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
26 </package>
27 <package name="hivclustering" version="1.2.3">
28 <repository changeset_revision="594976628691" name="package_python_3_4_hivclustering_1_2_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
29 </package>
30 <package name="tn93" version="1.0.2">
31 <repository changeset_revision="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
32 </package>
33 <package name="hivtrace" version="0.1.4">
34 <install version="1.0">
35 <actions>
36 <action type="download_by_url">https://github.com/veg/hivtrace/archive/0.1.4.tar.gz</action>
37 <action type="set_environment_for_install">
38 <repository changeset_revision="6e10967fdc7a" name="package_python_3_4_hyphy_2_2_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
39 <package name="hyphy" version="2.2.6" />
40 </repository>
41 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
42 <package name="pysam" version="0.8.3" />
43 </repository>
44 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
45 <package name="numpy" version="1.10.1" />
46 </repository>
47 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
48 <package name="biopython" version="1.66" />
49 </repository>
50 <repository changeset_revision="d71e21675123" name="package_python_3_4_bioext_0_17_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
51 <package name="bioext" version="0.17.3" />
52 </repository>
53 <repository changeset_revision="594976628691" name="package_python_3_4_hivclustering_1_2_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
54 <package name="hivclustering" version="1.2.3" />
55 </repository>
56 <repository changeset_revision="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
57 <package name="tn93" version="1.0.2" />
58 </repository>
59 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
60 <package name="python" version="3.4" />
61 </repository>
62 </action>
63 <action type="make_directory">$INSTALL_DIR/lib/python</action>
64 <action type="make_directory">$INSTALL_DIR/bin</action>
65 <action type="shell_command">
66 ln -s $PATH_PYTHON3/python3 $INSTALL_DIR/bin/python3 &amp;&amp;
67 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
68 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
69 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
70 $INSTALL_DIR/bin/python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
71 </action>
72 <action type="set_environment">
73 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
74 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
75 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
76 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOEXT]</environment_variable>
77 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
78 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
79 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
80 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
82 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_HIVCLUSTERING]</environment_variable>
83 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BIOEXT]</environment_variable>
84 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_TN93]</environment_variable>
85 </action>
86 </actions>
87 </install>
88 <readme>
89 This installs hivtrace 0.1.4 (and all its dependencies).
90
91 See usage instructions here: https://github.com/veg/hivtrace
92 </readme>
93 </package>
94 </tool_dependency>