Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_10

comparison tool_dependencies.xml @ 1:fde32464913e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_10 commit 5a986267144da2093f820e1833325fd3d5902c7d-dirty
author iuc
date Sun, 17 May 2015 16:35:04 -0400
parents 6a8a27d4992b
children f5929e04efc6
comparison
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0:6a8a27d4992b 1:fde32464913e
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.19"> 3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="numpy" version="1.9"> 6 <package name="numpy" version="1.9">
7 <repository changeset_revision="a095a5975d3a" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="1b7d6172a358" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="matplotlib" version="1.4"> 9 <package name="matplotlib" version="1.4">
10 <repository changeset_revision="652ee3afbd12" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="652ee3afbd12" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="scipy" version="0.14"> 12 <package name="scipy" version="0.14">
13 <repository changeset_revision="8d22fd5a704c" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="b24af010d80a" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="pysam" version="0.8.3"> 15 <package name="pysam" version="0.8.3">
16 <repository changeset_revision="d2acc22011f9" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="d2acc22011f9" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="bx-python" version="0.7.2"> 18 <package name="bx-python" version="0.7.2">
19 <repository changeset_revision="2ded28a666c7" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 19 <repository changeset_revision="2ded28a666c7" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
20 </package> 20 </package>
21 <package name="ucsc_tools" version="0.1"> 21 <package name="ucsc_tools" version="0.1">
22 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 22 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
23 </package> 23 </package>
24 <package name="python" version="2.7">
25 <repository changeset_revision="55bebb0e06ec" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
26 </package>
24 <package name="deepTools" version="1.5.9"> 27 <package name="deepTools" version="1.5.9">
25 <install version="1.0"> 28 <install version="1.0">
26 <actions> 29 <actions>
27 <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action> 30 <action type="setup_python_environment">
28 <action type="set_environment_for_install"> 31 <repository changeset_revision="55bebb0e06ec" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
32 <package name="python" version="2.7" />
33 </repository>
29 <repository changeset_revision="d2acc22011f9" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 34 <repository changeset_revision="d2acc22011f9" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
30 <package name="pysam" version="0.8.3" /> 35 <package name="pysam" version="0.8.3" />
31 </repository> 36 </repository>
32 <repository changeset_revision="2ded28a666c7" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 37 <repository changeset_revision="2ded28a666c7" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
33 <package name="bx-python" version="0.7.2" /> 38 <package name="bx-python" version="0.7.2" />
34 </repository> 39 </repository>
35 <repository changeset_revision="a095a5975d3a" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 40 <repository changeset_revision="1b7d6172a358" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
36 <package name="numpy" version="1.9" /> 41 <package name="numpy" version="1.9" />
37 </repository> 42 </repository>
38 <repository changeset_revision="652ee3afbd12" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 43 <repository changeset_revision="652ee3afbd12" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
39 <package name="matplotlib" version="1.4" /> 44 <package name="matplotlib" version="1.4" />
40 </repository> 45 </repository>
41 <repository changeset_revision="8d22fd5a704c" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 46 <repository changeset_revision="b24af010d80a" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
42 <package name="scipy" version="0.14" /> 47 <package name="scipy" version="0.14" />
43 </repository> 48 </repository>
44 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 49 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
45 <package name="samtools" version="0.1.19" /> 50 <package name="samtools" version="0.1.19" />
46 </repository> 51 </repository>
47 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 52 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
48 <package name="ucsc_tools" version="0.1" /> 53 <package name="ucsc_tools" version="0.1" />
49 </repository> 54 </repository>
50 </action> 55 <package>https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</package>
51 <action type="make_directory">$INSTALL_DIR/lib/python</action>
52 <action type="shell_command">
53 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
54 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
55 </action> 56 </action>
56 57
57 <action type="set_environment"> 58 <action type="set_environment">
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
59 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 60 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
60 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> 61 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
61 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 62 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
62 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable> 63 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
63 <!-- include samtools into PATH --> 64 <!-- include samtools into PATH -->
64 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable> 65 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>