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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_11 commit d094788c200e3ecf24f2a429000c888e82131ed1
author iuc
date Mon, 19 Oct 2015 16:58:29 -0400
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children 01eb49da8dcf
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-1:000000000000 0:315b83e21eea
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="numpy" version="1.9">
7 <repository changeset_revision="b4b823ad5f0f" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="matplotlib" version="1.4">
10 <repository changeset_revision="8f39fc9cadb1" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="scipy" version="0.14">
13 <repository changeset_revision="f9a80a69d278" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pysam" version="0.8.3">
16 <repository changeset_revision="ee642ed79a3b" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="bx-python" version="0.7.2">
19 <repository changeset_revision="8b54b30f3cd4" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
20 </package>
21 <package name="ucsc_tools" version="312">
22 <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
23 </package>
24 <package name="python" version="2.7.10">
25 <repository changeset_revision="b1a672a0df3c" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
26 </package>
27 <package name="deepTools" version="1.5.11">
28 <install version="1.0">
29 <actions>
30 <action type="setup_python_environment">
31 <repository changeset_revision="b1a672a0df3c" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
32 <package name="python" version="2.7.10" />
33 </repository>
34 <repository changeset_revision="ee642ed79a3b" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
35 <package name="pysam" version="0.8.3" />
36 </repository>
37 <repository changeset_revision="8b54b30f3cd4" name="package_python_2_7_bx_python_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
38 <package name="bx-python" version="0.7.2" />
39 </repository>
40 <repository changeset_revision="b4b823ad5f0f" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
41 <package name="numpy" version="1.9" />
42 </repository>
43 <repository changeset_revision="8f39fc9cadb1" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
44 <package name="matplotlib" version="1.4" />
45 </repository>
46 <repository changeset_revision="f9a80a69d278" name="package_python_2_7_scipy_0_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
47 <package name="scipy" version="0.14" />
48 </repository>
49 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
50 <package name="samtools" version="0.1.19" />
51 </repository>
52 <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
53 <package name="ucsc_tools" version="312" />
54 </repository>
55 <package>https://github.com/fidelram/deepTools/archive/1.5.11.tar.gz</package>
56 </action>
57
58 <action type="set_environment">
59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
60 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
61 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
62 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR</environment_variable>
63 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
64 <!-- include samtools into PATH -->
65 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
66 <!-- include numpy -->
67 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
68 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
69 <!-- include matplotlib -->
70 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
71 <!-- include scipy -->
72 <environment_variable action="prepend_to" name="PYTHONPATH">$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[PYTHONPATH_BX_PYTHON]</environment_variable>
76 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BX_PYTHON]</environment_variable>
77 <!-- include pysam -->
78 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
79 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
80 <!-- include ucsc tools -->
81 <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
82 <!-- libpng lib path -->
83 <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
84 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
85 <!-- disable the config file of deepTools -->
86 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
87 </action>
88 </actions>
89 </install>
90 <readme>
91 Installation of deepTools from Fidel Ramirez.
92 https://github.com/fidelram/deepTools
93 </readme>
94 </package>
95 </tool_dependency>