Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 27:bf1b1dcdd67b draft

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author bgruening
date Mon, 17 Mar 2014 16:23:58 -0400
parents 2ad3b027dfcd
children f7712a057440
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26:2ad3b027dfcd 27:bf1b1dcdd67b
5 </package> 5 </package>
6 <package name="numpy" version="1.7.1"> 6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="ef12a3a11d5b" 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="dceff6072512" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="d639ff3d6b6e" 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="984d208b0808" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="984d208b0808" 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">
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_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b"> 60 <package name="deepTools" version="1.5.4_43d3b51b3c3ab71dc07f31fefe6b3492226cc217">
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">
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"> 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" /> 73 <package name="numpy" version="1.7.1" />
74 </repository> 74 </repository>
75 <repository changeset_revision="dceff6072512" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> 75 <repository changeset_revision="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
76 <package name="matplotlib" version="1.2.1" /> 76 <package name="matplotlib" version="1.2.1" />
77 </repository> 77 </repository>
78 <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> 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" /> 79 <package name="scipy" version="0.12.0" />
80 </repository> 80 </repository>
81 </action> 81 </action>
82 <action type="shell_command">git reset --hard 3268f7e1458f3a520ab6fea3039971ee9d7a6d5b</action> 82 <action type="shell_command">git reset --hard 43d3b51b3c3ab71dc07f31fefe6b3492226cc217</action>
83 <action type="make_directory">$INSTALL_DIR/lib/python</action> 83 <action type="make_directory">$INSTALL_DIR/lib/python</action>
84 <action type="shell_command"> 84 <action type="shell_command">
85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
86 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
87 </action> 87 </action>