Mercurial > repos > pjbriggs > macs21

comparison tool_dependencies.xml @ 17:f346287fe52c draft

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author pjbriggs
date Tue, 26 Jul 2016 09:54:21 -0400
parents 062311890289
children 4e85d68a2347
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16:062311890289 17:f346287fe52c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <!-- Dependencies from main/test toolsheds --> 3 <!-- Dependencies from main/test toolsheds -->
4 <package name="numpy" version="1.9"> 4 <package name="numpy" version="1.9">
5 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 5 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
6 </package> 6 </package>
7 <package name="R" version="3.1.2"> 7 <package name="R" version="3.1.2">
8 <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 8 <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
9 </package> 9 </package>
10 <!-- Subset of UCSC tools --> 10 <!-- Subset of UCSC tools -->
11 <package name="ucsc_tools_for_macs21" version="1.0"> 11 <package name="ucsc_tools_for_macs21" version="1.0">
12 <install version="1.0"> 12 <install version="1.0">
13 <actions> 13 <actions>
43 <install version="1.0"> 43 <install version="1.0">
44 <actions> 44 <actions>
45 <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action> 45 <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
46 <!-- Install environment for main & test toolsheds --> 46 <!-- Install environment for main & test toolsheds -->
47 <action type="set_environment_for_install"> 47 <action type="set_environment_for_install">
48 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 48 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
49 <package name="numpy" version="1.9" /> 49 <package name="numpy" version="1.9" />
50 </repository>
51 <repository changeset_revision="4778b172b895" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
52 <package name="atlas" version="3.10.2" />
53 </repository> 50 </repository>
54 </action> 51 </action>
55 <action type="make_directory">$INSTALL_DIR/lib/python</action> 52 <action type="make_directory">$INSTALL_DIR/lib/python</action>
56 <action type="shell_command"> 53 <action type="shell_command">
57 echo PWD is: ;
58 pwd ;
59 echo PYTHONPATH is $PYTHONPATH ;
60 python -c "import numpy" ;
61 echo About to do the operations: ;
62 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 54 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
63 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 55 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
64 </action> 56 </action>
65 <action type="set_environment"> 57 <action type="set_environment">
66 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 58 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>