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Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author galaxyuser <galaxy_user@agr.g.ca>
date Mon, 10 Nov 2014 15:40:02 -0500
parents 95d75b35e4d2
children
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35:95d75b35e4d2 36:040410b8167e
1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page 1 Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
2 2
3 The Mothur Tool Suite repository:
4 - Provides Mothur wrappers for most Mothur tools
5 - Data type used by mothur and other metagenomics tools
6 - Downloads and builds Mothur on the Linux or Mac operating system
3 7
4 Mothur should be able to be auto-installed as a tool_dependency 8 Requirements:
5 You may want to reorganize the tool panel after installing 9 - Build utilities (make, GCC, gfortran, etc)
6 See below: Reorganize integrated_tool_panel.xml
7 This was based on: http://www.mothur.org/wiki/Mothur_manual
8 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands)
9 This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh
10 Requirements for auto installation:
11 - make (sudo-apt get install make)
12 - g++ (sudo apt-get install g++)
13 - gfortran (sudo apt-get install gfortran)
14 - pip (sudo apt-get install python-pip)
15 - simplejson (pip install simplejson) 10 - simplejson (pip install simplejson)
16 11
17 Repository Dependency: 12 Repository Dependency:
18 - BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/) 13 - BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)
19 - The repository name should be package_blast_2_2_26 so it matches with the tool dependency. 14 - The repository name should be package_blast_2_2_26 so it matches with the tool dependency.
20 15
21 16
22 Manual installation for Mothur: 17 Manual installation for Mothur:
112 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta 107 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
113 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax 108 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
114 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta 109 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
115 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax 110 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
116 111
117
118
119 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data) 112 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
120 tool-data/mothur_aligndb.loc 113 tool-data/mothur_aligndb.loc
121 tool-data/mothur_map.loc 114 tool-data/mothur_map.loc
122 tool-data/mothur_taxonomy.loc 115 tool-data/mothur_taxonomy.loc
123 tool-data/shared/jars/TreeVector.jar 116 tool-data/shared/jars/TreeVector.jar
124
125 117
126 ################################################################ 118 ################################################################
127 #### If you are manually adding this to your local galaxy: #### 119 #### If you are manually adding this to your local galaxy: ####
128 ################################################################ 120 ################################################################
129 121
130 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation 122 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
131 123
132
133 add datatype definition file: lib/galaxy/datatypes/metagenomics.py 124 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
134 125
135 add the following import line to: lib/galaxy/datatypes/registry.py 126 add the following import line to: lib/galaxy/datatypes/registry.py
136 import metagenomics # added for metagenomics mothur 127 import metagenomics # added for metagenomics mothur
137
138
139 128
140 add datatypes to: datatypes_conf.xml 129 add datatypes to: datatypes_conf.xml
141 130
142 add mothur tools to: tool_conf.xml 131 add mothur tools to: tool_conf.xml
143 132
170 # specifies files to copy to the new_file_path 159 # specifies files to copy to the new_file_path
171 # The list is separated by commas 160 # The list is separated by commas
172 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) 161 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
173 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output 162 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
174 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' 163 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
175
176 ##
177 ## NOTE: The "read" commands were eliminated with Mothur version 1.18
178 ##