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Mothur - updates for Mothur version 1.24
author Jim Johnson <jj@umn.edu>
date Wed, 28 Mar 2012 15:45:03 -0500
parents a6189f58fedb
children 5c77423823cb
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23:efd36aa39261 24:09740be2bc9c
1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page 1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page
2 2
3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands) 3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
4 4
5 Install mothur v.1.22.0 on your galaxy system so galaxy can execute the mothur command 5 Install mothur v.1.24.1 on your galaxy system so galaxy can execute the mothur command
6 ( This version of wrappers is designed for Mothur version 1.22 - it may work on later versions ) 6 ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions )
7 http://www.mothur.org/wiki/Download_mothur 7 http://www.mothur.org/wiki/Download_mothur
8 http://www.mothur.org/wiki/Installation 8 http://www.mothur.org/wiki/Installation
9 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) 9 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
10 10
11 TreeVector is also packaged with this Mothur package to view phylogenetic trees: 11 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
13 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol 13 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
14 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html 14 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
15 Install in galaxy: tool-data/shared/jars/TreeVector.jar 15 Install in galaxy: tool-data/shared/jars/TreeVector.jar
16 16
17 Install reference data from silva and greengenes 17 Install reference data from silva and greengenes
18 RDP reference file (modified for mothur):
19 http://www.mothur.org/wiki/RDP_reference_files
20 - 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.
21 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
22 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
23 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
24 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
25 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
18 Silva reference: 26 Silva reference:
19 http://www.mothur.org/wiki/Silva_reference_files 27 http://www.mothur.org/wiki/Silva_reference_files
20 - Bacterial references (14,956 sequences) 28 - Bacterial references (14,956 sequences)
21 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip 29 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
22 - Archaeal references (2,297 sequences) 30 - Archaeal references (2,297 sequences)
77 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta 85 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
78 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax 86 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
79 /project/db/galaxy/mothur/Silva.eukarya.zip 87 /project/db/galaxy/mothur/Silva.eukarya.zip
80 /project/db/galaxy/mothur/Gg_ss_map.zip 88 /project/db/galaxy/mothur/Gg_ss_map.zip
81 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta 89 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
82 90 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
83 91 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
84 Add tool-data: (contains pointers to silva and greengenes reference data) 92 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
93 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
94 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
95 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
96 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
97 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
98
99
100
101 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
85 tool-data/mothur_aligndb.loc 102 tool-data/mothur_aligndb.loc
86 tool-data/mothur_calulators.loc
87 tool-data/mothur_map.loc 103 tool-data/mothur_map.loc
88 tool-data/mothur_taxonomy.loc 104 tool-data/mothur_taxonomy.loc
89 tool-data/shared/jars/TreeVector.jar 105 tool-data/shared/jars/TreeVector.jar
90 106
91 107