Mercurial > repos > iuc > mothur_lefse
comparison README @ 0:1c04b0449893 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
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| date | Fri, 19 May 2017 05:27:50 -0400 |
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| -1:000000000000 | 0:1c04b0449893 |
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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 |