Mercurial > repos > bgruening > deeptools

comparison tool_dependencies.xml @ 29:3a2aab18a217 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 16 Sep 2014 13:46:05 -0400
parents f7712a057440
children 5231f398d784
comparison
equal deleted inserted replaced
28:f7712a057440 29:3a2aab18a217
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" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://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="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="https://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="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://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="https://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" prior_installation_required="True" 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="https://toolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="bx-python" version="12-2013"> 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" /> 19 <repository changeset_revision="55bd96a1c3b3" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
20 </package> 20 </package>
21 21
22 <package name="ucsc_tools" version="0.1"> 22 <package name="ucsc_tools" version="0.1">
23 <install version="1.0"> 23 <install version="1.0">
24 <actions> 24 <actions>
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="1.5.8_09023018b96c23f922aa2ea553090e9df8ecf41e"> 60 <package name="deepTools" version="1.5.9.1">
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">
66 <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="https://toolshed.g2.bx.psu.edu">
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="55bd96a1c3b3" name="package_bx_python_12_2013" owner="iuc" toolshed="https://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"> 72 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="https://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="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> 75 <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" toolshed="https://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="https://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 09023018b96c23f922aa2ea553090e9df8ecf41e</action> 82 <action type="shell_command">git reset --hard 351890e3db9a443484c5c349791b7247163cc94f</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>