Mercurial > repos > jetbrains > zinbra

annotate README.md @ 0:5f97f28e65ca

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial commit
author Oleg Shpynov <oleg.shpynov@gmail.com>
date Tue, 27 Oct 2015 14:20:42 +0300
parents
children 8cbb06892b62
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
1 Galaxy Applications
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
2 =================
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
3
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
4 Quick setup
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
5 ------------
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
6
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
7 * Download local copy of [galaxy](https://wiki.galaxyproject.org/Admin/GetGalaxy)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
8 * Checkout latest release: `git checkout release_15.01`
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
9 * Create `config/galaxy.ini` as a copy of `config/galaxy.ini.sample`
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
10 * Configure `tools_config_file`, `check_migrate_tools` properties
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
11 * Minimal `tool_conf.xml`
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
12 ```
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
13 <?xml version='1.0' encoding='utf-8'?>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
14 <toolbox>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
15 <section id="getext" name="Get Data">
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
16 <tool file="data_source/upload.xml" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
17 <tool file="data_source/ucsc_tablebrowser.xml" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
18 <tool file="data_source/ebi_sra.xml" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
19 <tool file="data_source/biomart.xml" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
20 </section>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
21 <section id="jetbrains" name="JetBrains tools">
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
22 <tool file="<PATH_TO_TOOLS>tools.xml" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
23 </section>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
24 </toolbox>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
25 ```
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
26
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
27 Useful links
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
28 ------------
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
29 * Galaxy
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
30 * [Develop apps](https://wiki.galaxyproject.org/Develop)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
31 * [Add tool tutorial](https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
32 * [Tool config format](https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
33 * [Quick reStructured text](http://docutils.sourceforge.net/docs/user/rst/quickref.html)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
34 * [Main tools Shed resource](https://toolshed.g2.bx.psu.edu/repository)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
35 * [Bed tools Shed example](https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_bedtools_2_24/tool_dependencies.xml)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
36 * [Biostar Galaxy](https://biostar.usegalaxy.org)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
37 * Biolabs
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
38 * Our [homepage](http://beta-research.jetbrains.org/groups/biolabs)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
39 * Our [wiki](http://biolabs.intellij.net)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
40 * Our NIH powered [genome browser](http://genomebrowser.labs.intellij.net)
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
41 * [TeamCity](https://teamcity.jetbrains.com/project.html?projectId=Epigenome)