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comparison README.md @ 0:5f97f28e65ca

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Initial commit
author Oleg Shpynov <oleg.shpynov@gmail.com>
date Tue, 27 Oct 2015 14:20:42 +0300
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children 8cbb06892b62
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1 Galaxy Applications
2 =================
3
4 Quick setup
5 ------------
6
7 * Download local copy of [galaxy](https://wiki.galaxyproject.org/Admin/GetGalaxy)
8 * Checkout latest release: `git checkout release_15.01`
9 * Create `config/galaxy.ini` as a copy of `config/galaxy.ini.sample`
10 * Configure `tools_config_file`, `check_migrate_tools` properties
11 * Minimal `tool_conf.xml`
12 ```
13 <?xml version='1.0' encoding='utf-8'?>
14 <toolbox>
15 <section id="getext" name="Get Data">
16 <tool file="data_source/upload.xml" />
17 <tool file="data_source/ucsc_tablebrowser.xml" />
18 <tool file="data_source/ebi_sra.xml" />
19 <tool file="data_source/biomart.xml" />
20 </section>
21 <section id="jetbrains" name="JetBrains tools">
22 <tool file="<PATH_TO_TOOLS>tools.xml" />
23 </section>
24 </toolbox>
25 ```
26
27 Useful links
28 ------------
29 * Galaxy
30 * [Develop apps](https://wiki.galaxyproject.org/Develop)
31 * [Add tool tutorial](https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial)
32 * [Tool config format](https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax)
33 * [Quick reStructured text](http://docutils.sourceforge.net/docs/user/rst/quickref.html)
34 * [Main tools Shed resource](https://toolshed.g2.bx.psu.edu/repository)
35 * [Bed tools Shed example](https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_bedtools_2_24/tool_dependencies.xml)
36 * [Biostar Galaxy](https://biostar.usegalaxy.org)
37 * Biolabs
38 * Our [homepage](http://beta-research.jetbrains.org/groups/biolabs)
39 * Our [wiki](http://biolabs.intellij.net)
40 * Our NIH powered [genome browser](http://genomebrowser.labs.intellij.net)
41 * [TeamCity](https://teamcity.jetbrains.com/project.html?projectId=Epigenome)