Mercurial > repos > yating-l > jbrowsearchivecreator

comparison tool_dependencies.xml @ 0:804a93e87cc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
author yating-l
date Wed, 12 Apr 2017 17:41:55 -0400
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children 25ad6770359e
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-1:000000000000 0:804a93e87cc8
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="1.2">
4 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6
7 <package name="numpy" version="1.9">
8 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package>
10
11 <package name="biopython" version="1.68">
12 <readme>
13 This package is based on package_biopython_1_67 owned by biopython.
14 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
15
16 This Galaxy Tool Shed package installs Biopython from source, having
17 first installed NumPy which is a build time depencency. This requires
18 and assumes a standard C compiler is already installed, along with
19 the Python header files.
20
21 Development of this dependency definition is being done here on GitHub:
22 https://github.com/biopython/galaxy_packages
23
24 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
25 </readme>
26 <install version="1.0">
27 <actions>
28 <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
29 <action type="set_environment_for_install">
30 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
31 <package name="numpy" version="1.9" />
32 </repository>
33 </action>
34 <action type="make_directory">$INSTALL_DIR/lib/python</action>
35 <action type="shell_command">
36 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
37 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
38 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
39 python setup.py install --install-lib $INSTALL_DIR/lib/python
40 </action>
41 <action type="set_environment">
42 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
43 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
44 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
45 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
46 </action>
47 </actions>
48 </install>
49 </package>
50
51 <package name="ucsc_tools_340" version="1.0">
52 <install version="1.0">
53 <actions_group>
54 <actions architecture="x86_64" os="linux">
55 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
56 <action type="move_directory_files">
57 <source_directory>.</source_directory>
58 <destination_directory>$INSTALL_DIR/bin</destination_directory>
59 </action>
60 </actions>
61 <action type="set_environment">
62 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
63 </action>
64 </actions_group>
65 </install>
66 <readme>The well known UCSC tools from Jim Kent.</readme>
67 </package>
68 <package name="jbrowse_tools" version="1.12.1">
69 <install version="1.0">
70 <actions_group>
71 <actions architecture="x86_64" os="linux">
72 <action type="download_by_url">http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=105</action>
73 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
74 <action type="shell_command">
75 ./setup.sh
76 </action>
77 <action type="move_directory_files">
78 <source_directory>.</source_directory>
79 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
80 </action>
81 <action type="set_environment">
82 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
83 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
84 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
85 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
86 </action>
87 </actions>
88 </actions_group>
89 </install>
90 <readme>The perl scripts for converting flat files to json.</readme>
91 </package>
92
93
94 </tool_dependency>