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comparison README @ 0:0468cb2dd83e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:51:37 -0400
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1 Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
2
3 The Mothur Tool Suite repository:
4 - Provides Mothur wrappers for the Mothur tools
5 - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system
6
7 Installing Tools via the API:
8 This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead
9 - Install ephemeris: pip install ephemeris -U
10 - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml
11 - (You can find a tools.yaml you can use in this repo as well)
12
13 Installing reference data from silva and greengenes:
14 - There is a Galaxy datamanager for available for Mothur
15
16 RDP reference file (modified for mothur):
17 http://www.mothur.org/wiki/RDP_reference_files
18 - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
19 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
20 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
21 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
22 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
23 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
24 Silva reference:
25 http://www.mothur.org/wiki/Silva_reference_files
26 - Bacterial references (14,956 sequences)
27 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
28 - Archaeal references (2,297 sequences)
29 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
30 - Eukaryotic references (1,238 sequences)
31 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
32 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
33 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
34 Alignment database rRNA gene sequences:
35 http://www.mothur.org/wiki/Alignment_database
36 - greengenes reference alignment
37 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
38 - SILVA (Silva reference)
39 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
40 Secondary structure mapping files:
41 http://www.mothur.org/wiki/Secondary_structure_map
42 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
43 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
44 Lane masks:
45 http://www.mothur.org/wiki/Lane_mask
46 greengenes-compatible mask:
47 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
48 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
49 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
50 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
51 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
52 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
53 SILVA-compatible mask:
54 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
55 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
56 Lookup Files for sff flow analysis using shhh.flows:
57 http://www.mothur.org/wiki/Alignment_database