Mercurial > repos > dpryan79 > package_python_2_7_bwameth_0_20

comparison tool_dependencies.xml @ 3:435f9d24c060 draft

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author dpryan79
date Wed, 14 Sep 2016 07:24:38 -0400
parents 831f8397a424
children 44d16fcc7347
comparison
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2:831f8397a424 3:435f9d24c060
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="python" version="2.7.10">
4 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
3 <package name="bwa" version="0.7.12"> 6 <package name="bwa" version="0.7.12">
4 <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 8 </package>
6 <package name="samtools" version="1.2"> 9 <package name="samtools" version="1.2">
7 <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 11 </package>
9 <package name="python" version="2.7.10"> 12 <package name="toolshed" version="0.4.6">
10 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="c0ca6d5a5c5c" name="package_python_2_7_toolshed_0_4_6" owner="dpryan79" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 14 </package>
12 <package name="bwameth" version="0.20"> 15 <package name="bwameth" version="0.20">
13 <install version="1.0"> 16 <install version="1.0">
14 <actions> 17 <actions>
15 <action type="setup_python_environment"> 18 <action type="setup_python_environment">
16 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 19 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
17 <package name="python" version="2.7.10" /> 20 <package name="python" version="2.7.10" />
18 </repository> 21 </repository>
22 <package md5sum="7d6e2ed375da0fc3d44de3477aa5c087">https://github.com/brentp/bwa-meth/archive/v0.2.0.tar.gz</package>
19 </action> 23 </action>
20 <action type="set_environment"> 24 <action type="set_environment">
25 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 26 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
22 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
23 </action> 27 </action>
24 <action type="make_directory">$INSTALL_DIR/lib/python</action>
25 <action type="shell_command">git clone https://github.com/brentp/bwa-meth &amp;&amp; cd bwa-meth &amp;&amp; git reset --hard 7dfec747105b9fa2cf1678bf5f67e860a0155d0e &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
26 </actions> 28 </actions>
27 </install> 29 </install>
28 <readme> 30 <readme>
29 Installation of bwa-meth from Brent Pedersen 31 Installation of toolshed from Brent Pedersen
30 https://github.com/brentp/bwa-meth 32 https://github.com/brentp/toolshed
31 </readme> 33 </readme>
32 </package> 34 </package>
33 </tool_dependency> 35 </tool_dependency>