Mercurial > repos > yating-l > jbrowsearchivecreator

comparison tool_dependencies.xml @ 6:237707a6b74d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
parents 25ad6770359e
children 5d5fdcb798da
comparison
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5:e762f4b9e4bd 6:237707a6b74d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="1.2"> 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" /> 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="ucsc_hac" version="340">
8 <repository changeset_revision="1a15120c22c8" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 9 </package>
6 10
7 <package name="numpy" version="1.9"> 11 <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" /> 12 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package> 13 </package>
45 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> 49 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
46 </action> 50 </action>
47 </actions> 51 </actions>
48 </install> 52 </install>
49 </package> 53 </package>
50 54
51 <package name="ucsc_tools_340" version="1.0"> 55 <package name="jbrowse_tools" version="1.12.4">
52 <install version="1.0"> 56 <install version="1.0">
53 <actions_group> 57 <actions_group>
54 <actions architecture="x86_64" os="linux"> 58 <actions architecture="x86_64" os="linux">
55 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action> 59 <action type="download_by_url">https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4.zip</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">$INSTALL_DIR/jbrowse</action> 60 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
74 <action type="set_environment">
75 <environment_variable action="set_to" name="HOME">$INSTALL_DIR/jbrowse</environment_variable>
76 </action>
77 <action type="shell_command"> 61 <action type="shell_command">
78 export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh 62 export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh
79 </action> 63 </action>
80 <action type="move_directory_files"> 64 <action type="move_directory_files">
81 <source_directory>.</source_directory> 65 <source_directory>.</source_directory>
91 </actions_group> 75 </actions_group>
92 </install> 76 </install>
93 <readme>The perl scripts for converting flat files to json.</readme> 77 <readme>The perl scripts for converting flat files to json.</readme>
94 </package> 78 </package>
95 79
96
97 </tool_dependency> 80 </tool_dependency>