Mercurial > repos > iuc > package_deeptools_1_5_9

comparison tool_dependencies.xml @ 0:4294ef121f97 draft

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author iuc
date Thu, 26 Feb 2015 07:38:25 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="deepTools" version="1.5.9">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
7 <action type="set_environment_for_install">
8 <repository changeset_revision="64e2daea7b15" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
9 <package name="pysam" version="0.7.7" />
10 </repository>
11 <repository changeset_revision="4c15bd2528e1" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
12 <package name="bx-python" version="0.7.1" />
13 </repository>
14 <repository changeset_revision="6a7842f2f960" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
15 <package name="numpy" version="1.7.1" />
16 </repository>
17 <repository changeset_revision="b08a9f0f28ec" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="matplotlib" version="1.2.1" />
19 </repository>
20 <repository changeset_revision="6d8201c2a767" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 <package name="scipy" version="0.12.0" />
22 </repository>
23 <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="samtools" version="0.1.19" />
25 </repository>
26 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
27 <package name="ucsc_tools" version="0.1" />
28 </repository>
29 </action>
30 <action type="make_directory">$INSTALL_DIR/lib/python</action>
31 <action type="shell_command">
32 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
33 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
34 </action>
35
36 <action type="set_environment">
37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
38 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
39 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
40 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
41 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
42 <!-- include samtools into PATH -->
43 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
44 <!-- include numpy -->
45 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
46 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
47 <!-- include matplotlib -->
48 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
49 <!-- include scipy -->
50 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
51 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
52 <!-- include bx-python -->
53 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
54 <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
55 <!-- include pysam -->
56 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
57 <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
58 <!-- include ucsc tools -->
59 <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
60
61 <!-- disable the config file of deepTools -->
62 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
63 </action>
64 </actions>
65 </install>
66 <readme>
67 Installation of deepTools from Fidel Ramirez.
68 https://github.com/fidelram/deepTools
69 </readme>
70 </package>
71 </tool_dependency>