Mercurial > repos > pjbriggs > macs21

comparison tool_dependencies.xml @ 0:06cb587a5e87 draft

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Uploaded initial version 2.1.0-4.
author pjbriggs
date Tue, 30 Jun 2015 08:16:18 -0400
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children 02a01ea54722
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-1:000000000000 0:06cb587a5e87
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <!-- Dependencies from main/test toolsheds -->
4 <package name="numpy" version="1.9">
5 <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
6 </package>
7 <package name="R" version="3.1.2">
8 <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package>
10 <!-- Subset of UCSC tools -->
11 <package name="ucsc_tools_for_macs21" version="1.0">
12 <install version="1.0">
13 <actions>
14 <!-- fetchChromSizes -->
15 <action type="download_binary">
16 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
17 </action>
18 <action type="chmod">
19 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
20 </action>
21 <!-- bedClip -->
22 <action type="download_binary">
23 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
24 </action>
25 <action type="chmod">
26 <file mode="755">$INSTALL_DIR/bedClip</file>
27 </action>
28 <!-- bedGraphToBigWig -->
29 <action type="download_binary">
30 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
31 </action>
32 <action type="chmod">
33 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
34 </action>
35 <action type="set_environment">
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
37 </action>
38 </actions>
39 </install>
40 </package>
41 <!-- MACS 2.1.0 -->
42 <package name="macs2" version="2.1.0.20140616">
43 <install version="1.0">
44 <actions>
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 -->
47 <action type="set_environment_for_install">
48 <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
49 <package name="numpy" version="1.9" />
50 </repository>
51 </action>
52 <action type="make_directory">$INSTALL_DIR/lib/python</action>
53 <action type="shell_command">
54 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
55 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
56 </action>
57 <action type="set_environment">
58 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
60 </action>
61 </actions>
62 </install>
63 <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme>
64 </package>
65 </tool_dependency>