Mercurial > repos > yhoogstrate > package_crossmap_0_2
comparison tool_dependencies.xml @ 3:bbc4d67d6a37 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1
author | yhoogstrate |
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date | Thu, 12 Nov 2015 09:06:02 -0500 |
parents | e4de7f1284ce |
children | dbe83f5bef40 |
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2:e4de7f1284ce | 3:bbc4d67d6a37 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool_dependency> | 2 <tool_dependency> |
3 <package name="python" version="2.7.10"> | |
4 <repository changeset_revision="73631e818d3d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
5 </package> | |
3 <package name="nose" version="1.3.7"> | 6 <package name="nose" version="1.3.7"> |
4 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | 7 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
5 </package> | 8 </package> |
6 | |
7 <package name="numpy" version="1.9"> | 9 <package name="numpy" version="1.9"> |
8 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | 10 <repository changeset_revision="c1e72cd24a9c" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
9 </package> | 11 </package> |
10 | |
11 <package name="cython" version="0.23.1"> | 12 <package name="cython" version="0.23.1"> |
12 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | 13 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
13 </package> | 14 </package> |
14 | 15 |
15 <package name="crossmap" version="0.2"> | 16 <package name="crossmap" version="0.2"> |
16 <install version="1.0"> | 17 <install version="1.0"> |
17 <actions> | 18 <actions> |
18 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action> | 19 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action> |
19 | 20 |
20 <action type="setup_python_environment"> | 21 <action type="setup_python_environment"> |
22 <repository changeset_revision="73631e818d3d" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
23 <package name="python" version="2.7.10" /> | |
24 </repository> | |
21 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> | 25 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> |
22 <package name="nose" version="1.3.7" /> | 26 <package name="nose" version="1.3.7" /> |
23 </repository> | 27 </repository> |
24 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | 28 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
25 <package name="cython" version="0.23.1" /> | 29 <package name="cython" version="0.23.1" /> |
26 </repository> | 30 </repository> |
27 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | 31 <repository changeset_revision="c1e72cd24a9c" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
28 <package name="numpy" version="1.9" /> | 32 <package name="numpy" version="1.9" /> |
29 </repository> | 33 </repository> |
30 </action> | 34 </action> |
31 | 35 |
32 <!-- If CrossMap is installed with - - home or - - prefix | 36 <!-- If CrossMap is installed with - - home or - - prefix |
33 into, it often crashes with a 'write-test' error | 37 it often crashes with a 'write-test' error |
34 | 38 |
35 Using - - root places the installation in: | 39 Using - - root places the installation in: |
36 $INSTALL_DIR / (python path dir) / | 40 $INSTALL_DIR / (python path dir) / |
37 --> | 41 --> |
38 <action type="shell_command"> | 42 <action type="shell_command"> |
43 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib && | 47 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib && |
44 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin | 48 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin |
45 </action> | 49 </action> |
46 | 50 |
47 <action type="set_environment"> | 51 <action type="set_environment"> |
48 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable> | 52 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable> |
49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | 53 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
50 | 54 |
51 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable> | 55 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable> |
52 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> | 56 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> |
53 </action> | 57 </action> |