Mercurial > repos > pjbriggs > macs21

comparison tool_dependencies.xml @ 2:15889783e759 draft

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Fix bugs in tool operation and update dependencies.
author pjbriggs
date Thu, 12 Feb 2015 08:29:07 -0500
parents d0986d2be693
children 881a48588832
comparison
equal deleted inserted replaced
1:d0986d2be693 2:15889783e759
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="python" version="2.7"> 3 <!-- Dependencies from local toolshed
4 <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <package name="numpy" version="1.9">
5 <repository name="package_numpy_1_9" prior_installation_required="True" owner="pjbriggs" />
5 </package> 6 </package>
6 <package name="numpy" version="1.8.1"> 7 -->
7 <repository changeset_revision="0f9f634dec8a" name="package_numpy_1_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 8 <!-- Dependencies from main/test toolsheds -->
9 <package name="numpy" version="1.9">
10 <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 11 </package>
12 <!-- Subset of UCSC tools -->
13 <package name="ucsc_tools" version="1.0">
14 <install version="1.0">
15 <actions>
16 <!-- fetchChromSizes -->
17 <action type="download_binary">
18 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
19 </action>
20 <action type="chmod">
21 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
22 </action>
23 <!-- bedClip -->
24 <action type="download_binary">
25 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
26 </action>
27 <action type="chmod">
28 <file mode="755">$INSTALL_DIR/bedClip</file>
29 </action>
30 <!-- bedGraphToBigWig -->
31 <action type="download_binary">
32 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
33 </action>
34 <action type="chmod">
35 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
36 </action>
37 </actions>
38 </install>
39 </package>
40 <!-- MACS 2.1.0 -->
9 <package name="macs2" version="2.1.0.20140616"> 41 <package name="macs2" version="2.1.0.20140616">
10 <install version="1.0"> 42 <install version="1.0">
11 <actions> 43 <actions>
12 <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action> 44 <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
13 <action type="set_environment_for_install"> 45 <!-- Install environment for local toolshed
14 <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 46 <repository name="package_numpy_1_9" owner="pjbriggs">
15 <package name="python" version="2.7" /> 47 <package name="python_numpy" version="1.9" />
16 </repository>
17 <repository changeset_revision="0f9f634dec8a" name="package_numpy_1_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="numpy" version="1.8.1" />
19 </repository> 48 </repository>
20 </action> 49 </action>
50 -->
51 <!-- Install environment for main & test toolsheds -->
52 <action type="set_environment_for_install">
53 <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
54 <package name="numpy" version="1.9" />
55 </repository>
56 </action>
57 --&gt;
21 <action type="make_directory">$INSTALL_DIR/lib/python</action> 58 <action type="make_directory">$INSTALL_DIR/lib/python</action>
22 <action type="shell_command"> 59 <action type="shell_command">
23 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 60 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
24 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin 61 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
25 </action> 62 </action>