Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_10

comparison tool_dependencies.xml @ 0:6a8a27d4992b 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 15:01:25 -0400
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children fde32464913e
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-1:000000000000 0:6a8a27d4992b
1 <?xml version="1.0"?>
2 <tool_dependency>
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" />
5 </package>
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" />
8 </package>
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" />
11 </package>
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" />
14 </package>
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" />
17 </package>
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" />
20 </package>
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" />
23 </package>
24 <package name="deepTools" version="1.5.9">
25 <install version="1.0">
26 <actions>
27 <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
28 <action type="set_environment_for_install">
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">
30 <package name="pysam" version="0.8.3" />
31 </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">
33 <package name="bx-python" version="0.7.2" />
34 </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">
36 <package name="numpy" version="1.9" />
37 </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">
39 <package name="matplotlib" version="1.4" />
40 </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">
42 <package name="scipy" version="0.14" />
43 </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">
45 <package name="samtools" version="0.1.19" />
46 </repository>
47 <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" />
49 </repository>
50 </action>
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 $INSTALL_DIR/bin
55 </action>
56
57 <action type="set_environment">
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
59 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
60 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
61 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
62 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
63 <!-- include samtools into PATH -->
64 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
65 <!-- include numpy -->
66 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
67 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
68 <!-- include matplotlib -->
69 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
70 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[MATPLOTLIB_LIB_PATH]</environment_variable>
71 <!-- include scipy -->
72 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
73 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
74 <!-- include bx-python -->
75 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
76 <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
77 <!-- include pysam -->
78 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
79 <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
80 <!-- include ucsc tools -->
81 <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
82
83 <!-- disable the config file of deepTools -->
84 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
85 </action>
86 </actions>
87 </install>
88 <readme>
89 Installation of deepTools from Fidel Ramirez.
90 https://github.com/fidelram/deepTools
91 </readme>
92 </package>
93 </tool_dependency>