Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 13:b4c5dd45778a draft

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Uploaded
author bgruening
date Mon, 16 Dec 2013 04:36:19 -0500
parents 135f3bae5c56
children ef65d6b68ccc
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12:aea72b24dea0 13:b4c5dd45778a
55 </actions> 55 </actions>
56 </install> 56 </install>
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> 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>
58 </package> 58 </package>
59 59
60 <package name="deepTools" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49"> 60 <package name="deepTools" version="1.5.4_74aac0843a956ca352e3e85087f20c8f158e2f7d">
61 <install version="1.0"> 61 <install version="1.0">
62 <actions> 62 <actions>
63 <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>
64 <!-- populate the environment variables from the dependend repos --> 64 <!-- populate the environment variables from the dependend repos -->
65 <action type="set_environment_for_install"> 65 <action type="set_environment_for_install">
67 <package name="pysam" version="0.7.7" /> 67 <package name="pysam" version="0.7.7" />
68 </repository> 68 </repository>
69 <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> 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" /> 70 <package name="bx-python" version="12-2013" />
71 </repository> 71 </repository>
72 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
73 <package name="numpy" version="1.7.1" />
74 </repository>
75 <repository changeset_revision="dceff6072512" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
76 <package name="matplotlib" version="1.2.1" />
77 </repository>
78 <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
79 <package name="scipy" version="0.12.0" />
80 </repository>
72 </action> 81 </action>
73 <action type="shell_command">git reset --hard 6765c227d9628f8e6ba690e6fde7f1d86c497b49</action> 82 <action type="shell_command">git reset --hard 74aac0843a956ca352e3e85087f20c8f158e2f7d</action>
74 <action type="make_directory">$INSTALL_DIR/lib/python</action> 83 <action type="make_directory">$INSTALL_DIR/lib/python</action>
75 <action type="shell_command"> 84 <action type="shell_command">
76 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
77 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 86 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
78 </action> 87 </action>