Mercurial > repos > george-weingart > lefse
comparison Readme_lefse_Galaxy.txt @ 0:e7cd19afda2e draft
Lefse
author | george-weingart |
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date | Tue, 13 May 2014 21:57:00 -0400 |
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-1:000000000000 | 0:e7cd19afda2e |
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1 Installation instructions for lefse in a galaxy environment. | |
2 These instructions require the Mercurial versioning system, galaxy, and an internet connection. | |
3 | |
4 1. In the "galaxy-dist/tools" directory install lefse by cloning the repository: | |
5 | |
6 bitbucket.org/biobakery/lefse_galaxy | |
7 | |
8 2. Rename the galaxy_lefse directory thus created to "lefse" | |
9 | |
10 3. Update member tool_conf.xml in the galaxy directory adding the following: | |
11 | |
12 <section name="LEfSe" id="lefse"> | |
13 <tool file="lefse/format_input.xml" /> | |
14 <tool file="lefse/run_lefse.xml" /> | |
15 <tool file="lefse/plot_res.xml" /> | |
16 <tool file="lefse/plot_cladogram.xml" /> | |
17 <tool file="lefse/plot_single_feature.xml" /> | |
18 <tool file="lefse/plot_features.xml" /> | |
19 </section> | |
20 | |
21 | |
22 4. Update member datatypes_conf.xml in the galaxy directory adding the following: | |
23 <datatype extension="lefse" type="galaxy.datatypes.data:Lefse" display_in_upload="true"/> | |
24 <datatype extension="lefse_res" type="galaxy.datatypes.tabular:LefseRes" display_in_upload="true"/> | |
25 | |
26 5. Copy the *.png members to galaxy-dist/static/images | |
27 | |
28 6. Recycle galaxy | |
29 |