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comparison tool_dependencies.xml @ 65:9bee2c86eeb1 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
author iuc
date Mon, 25 May 2015 05:16:10 -0400
parents 627004611e98
children 1dbd76a58d8b
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64:627004611e98 65:9bee2c86eeb1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.19"> 3 <package name="deepTools" version="1.5.10">
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="41de4f005517" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="matplotlib" version="1.2.1">
10 <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="scipy" version="0.12.0">
13 <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pysam" version="0.7.7">
16 <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="bx-python" version="0.7.1">
19 <repository changeset_revision="ec30e3f438f4" name="package_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="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
30 <package name="pysam" version="0.7.7" />
31 </repository>
32 <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
33 <package name="bx-python" version="0.7.1" />
34 </repository>
35 <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
36 <package name="numpy" version="1.7.1" />
37 </repository>
38 <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
39 <package name="matplotlib" version="1.2.1" />
40 </repository>
41 <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
42 <package name="scipy" version="0.12.0" />
43 </repository>
44 <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" 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> 6 </tool_dependency>