Mercurial > repos > iuc > mothur_classify_seqs
diff README @ 0:2a0d8b8c3ade 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 05:13:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri May 19 05:13:36 2017 -0400 @@ -0,0 +1,57 @@ +Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page) + +The Mothur Tool Suite repository: + - Provides Mothur wrappers for the Mothur tools + - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system + +Installing Tools via the API: +This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead + - Install ephemeris: pip install ephemeris -U + - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml + - (You can find a tools.yaml you can use in this repo as well) + +Installing reference data from silva and greengenes: + - There is a Galaxy datamanager for available for Mothur + + RDP reference file (modified for mothur): + http://www.mothur.org/wiki/RDP_reference_files + - 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. + http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip + - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales + http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip + - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab + http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip + Silva reference: + http://www.mothur.org/wiki/Silva_reference_files + - Bacterial references (14,956 sequences) + http://www.mothur.org/w/images/9/98/Silva.bacteria.zip + - Archaeal references (2,297 sequences) + http://www.mothur.org/w/images/3/3c/Silva.archaea.zip + - Eukaryotic references (1,238 sequences) + http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip + - Silva-based alignment of template file for chimera.slayer (5,181 sequences) + http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip + Alignment database rRNA gene sequences: + http://www.mothur.org/wiki/Alignment_database + - greengenes reference alignment + http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip + - SILVA (Silva reference) + http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip + Secondary structure mapping files: + http://www.mothur.org/wiki/Secondary_structure_map + http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip + http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip + Lane masks: + http://www.mothur.org/wiki/Lane_mask + greengenes-compatible mask: + - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database + http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter + - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database + http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter + - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper + http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter + SILVA-compatible mask: + - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper + http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter + Lookup Files for sff flow analysis using shhh.flows: + http://www.mothur.org/wiki/Alignment_database