Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 9:c53a73b8eef9 draft

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Uploaded
author bgruening
date Tue, 10 Dec 2013 12:13:18 -0500
parents 1ee0b1ecf500
children 135f3bae5c56
comparison
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8:1c5ed9126db6 9:c53a73b8eef9
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="samtools" version="0.1.19">
4 <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="numpy" version="1.7.1"> 6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="matplotlib" version="1.2.1"> 9 <package name="matplotlib" version="1.2.1">
10 <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="scipy" version="0.12.0"> 12 <package name="scipy" version="0.12.0">
13 <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="pysam" version="0.7.7"> 15 <package name="pysam" version="0.7.7">
16 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
17 </package>
18 <package name="bx-python" version="12-2013">
19 <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
17 </package> 20 </package>
18 21
19 <package name="ucsc_tools" version="0.1"> 22 <package name="ucsc_tools" version="0.1">
20 <install version="1.0"> 23 <install version="1.0">
21 <actions> 24 <actions>
52 </actions> 55 </actions>
53 </install> 56 </install>
54 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> 57 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
55 </package> 58 </package>
56 59
57 <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a"> 60 <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">
58 <install version="1.0"> 61 <install version="1.0">
59 <actions> 62 <actions>
60 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> 63 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
61 <!-- populate the environment variables from the dependend repos --> 64 <!-- populate the environment variables from the dependend repos -->
62 <action type="set_environment_for_install"> 65 <action type="set_environment_for_install">
63 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> 66 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
64 <package name="pysam" version="0.7.7" /> 67 <package name="pysam" version="0.7.7" />
65 </repository> 68 </repository>
69 <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
70 <package name="bx-python" version="12-2013" />
71 </repository>
66 </action> 72 </action>
67 <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action> 73 <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action>
68 <action type="make_directory">$INSTALL_DIR/lib/python</action> 74 <action type="make_directory">$INSTALL_DIR/lib/python</action>
69 <action type="shell_command"> 75 <action type="shell_command">
70 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 76 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
71 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 77 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
72 </action> 78 </action>
76 <!-- disable the config file of deepTools --> 82 <!-- disable the config file of deepTools -->
77 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> 83 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
78 </action> 84 </action>
79 </actions> 85 </actions>
80 </install> 86 </install>
81 <readme>Installation of deepTools from Fidel Ramirez.</readme> 87 <readme>
88 Installation of deepTools from Fidel Ramirez.
89 https://github.com/fidelram/deepTools
90 </readme>
82 </package> 91 </package>
83 </tool_dependency> 92 </tool_dependency>