Mercurial > repos > nml > package_python_3_4_hivtrace_0_1_4
comparison tool_dependencies.xml @ 0:38541eaf0d20 draft
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 |
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date | Thu, 07 Jul 2016 09:58:46 -0400 |
parents | |
children | af0cf1f508fa |
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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 $INSTALL_DIR/bin/python3 && | |
67 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
68 export PATH=$PATH:$PATH_NUMPY && | |
69 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && | |
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> |