Mercurial > repos > jjohnson > mothur_toolsuite

comparison mothur/README @ 15:a6189f58fedb

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Mothur - updated for Mothur version 1.22.0
author Jim Johnson <jj@umn.edu>
date Tue, 08 Nov 2011 11:45:32 -0600
parents 7bfe1f843858
children 09740be2bc9c
comparison
equal deleted inserted replaced
14:ee59e5cff3ba 15:a6189f58fedb
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 Install mothur v.1.20.0 on your galaxy system so galaxy can execute the mothur command 3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
4 ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions ) 4
5 Install mothur v.1.22.0 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 )
5 http://www.mothur.org/wiki/Download_mothur 7 http://www.mothur.org/wiki/Download_mothur
6 http://www.mothur.org/wiki/Installation 8 http://www.mothur.org/wiki/Installation
7 ( 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 )
8 10
9 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:
43 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper 45 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
44 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter 46 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
45 SILVA-compatible mask: 47 SILVA-compatible mask:
46 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper 48 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
47 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter 49 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
50 Lookup Files for sff flow analysis using shhh.flows:
51 http://www.mothur.org/wiki/Alignment_database
48 52
49 Example from UMN installation: (We also made these available in a Galaxy public data library) 53 Example from UMN installation: (We also made these available in a Galaxy public data library)
50 /project/db/galaxy/mothur/Silva.bacteria.zip 54 /project/db/galaxy/mothur/Silva.bacteria.zip
51 /project/db/galaxy/mothur/silva.eukarya.fasta 55 /project/db/galaxy/mothur/silva.eukarya.fasta
52 /project/db/galaxy/mothur/Greengenes.alignment.zip 56 /project/db/galaxy/mothur/Greengenes.alignment.zip
115 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/> 119 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
116 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/> 120 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
117 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/> 121 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
118 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/> 122 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
119 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/> 123 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
124 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
125 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
126 </datatype>
120 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/> 127 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
121 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/> 128 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
122 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/> 129 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
123 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/> 130 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
124 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/> 131 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
125 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/> 132 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
126 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/> 133 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
127 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/> 134 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
128 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/> 135 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
129 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/> 136 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
137 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
130 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> 138 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
131 <!-- End Mothur Datatypes --> 139 <!-- End Mothur Datatypes -->
132 140
133 add mothur tools to: tool_conf.xml 141 add mothur tools to: tool_conf.xml
134 <section name="Metagenomics Mothur" id="metagenomics_mothur"> 142 <section name="Metagenomics Mothur" id="metagenomics_mothur">
136 <tool file="mothur/merge.files.xml"/> 144 <tool file="mothur/merge.files.xml"/>
137 <tool file="mothur/make.group.xml"/> 145 <tool file="mothur/make.group.xml"/>
138 <tool file="mothur/get.groups.xml"/> 146 <tool file="mothur/get.groups.xml"/>
139 <tool file="mothur/remove.groups.xml"/> 147 <tool file="mothur/remove.groups.xml"/>
140 <tool file="mothur/merge.groups.xml"/> 148 <tool file="mothur/merge.groups.xml"/>
149 <tool file="mothur/count.groups.xml"/>
141 <tool file="mothur/make.design.xml"/> 150 <tool file="mothur/make.design.xml"/>
142 <tool file="mothur/sub.sample.xml"/> 151 <tool file="mothur/sub.sample.xml"/>
143 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> 152 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
144 <tool file="mothur/sffinfo.xml"/> 153 <tool file="mothur/sffinfo.xml"/>
154 <tool file="mothur/trim.flows.xml"/>
155 <tool file="mothur/shhh.flows.xml"/>
145 <tool file="mothur/make.fastq.xml"/> 156 <tool file="mothur/make.fastq.xml"/>
146 <tool file="mothur/fastq.info.xml"/> 157 <tool file="mothur/fastq.info.xml"/>
147 <tool file="mothur/summary.seqs.xml"/> 158 <tool file="mothur/summary.seqs.xml"/>
148 <tool file="mothur/count.seqs.xml"/> 159 <tool file="mothur/count.seqs.xml"/>
149 <tool file="mothur/reverse.seqs.xml"/> 160 <tool file="mothur/reverse.seqs.xml"/>
167 <tool file="mothur/pcoa.xml"/> 178 <tool file="mothur/pcoa.xml"/>
168 <tool file="mothur/pca.xml"/> 179 <tool file="mothur/pca.xml"/>
169 <tool file="mothur/nmds.xml"/> 180 <tool file="mothur/nmds.xml"/>
170 <tool file="mothur/corr.axes.xml"/> 181 <tool file="mothur/corr.axes.xml"/>
171 <tool file="mothur/classify.seqs.xml"/> 182 <tool file="mothur/classify.seqs.xml"/>
183 <tool file="mothur/seq.error.xml"/>
172 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/> 184 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
173 <tool file="mothur/chimera.bellerophon.xml"/> 185 <tool file="mothur/chimera.bellerophon.xml"/>
174 <tool file="mothur/chimera.ccode.xml"/> 186 <tool file="mothur/chimera.ccode.xml"/>
175 <tool file="mothur/chimera.check.xml"/> 187 <tool file="mothur/chimera.check.xml"/>
176 <tool file="mothur/chimera.pintail.xml"/> 188 <tool file="mothur/chimera.pintail.xml"/>
198 <tool file="mothur/get.relabund.xml"/> 210 <tool file="mothur/get.relabund.xml"/>
199 <tool file="mothur/make.shared.xml"/> 211 <tool file="mothur/make.shared.xml"/>
200 <tool file="mothur/get.group.xml"/> 212 <tool file="mothur/get.group.xml"/>
201 <tool file="mothur/bin.seqs.xml"/> 213 <tool file="mothur/bin.seqs.xml"/>
202 <tool file="mothur/get.sharedseqs.xml"/> 214 <tool file="mothur/get.sharedseqs.xml"/>
215 <tool file="mothur/summary.tax.xml"/>
203 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> 216 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
204 <tool file="mothur/collect.single.xml"/> 217 <tool file="mothur/collect.single.xml"/>
205 <tool file="mothur/rarefaction.single.xml"/> 218 <tool file="mothur/rarefaction.single.xml"/>
206 <tool file="mothur/summary.single.xml"/> 219 <tool file="mothur/summary.single.xml"/>
207 <tool file="mothur/heatmap.bin.xml"/> 220 <tool file="mothur/heatmap.bin.xml"/>
233 <tool file="mothur/indicator.xml"/> 246 <tool file="mothur/indicator.xml"/>
234 <tool file="mothur/deunique.tree.xml"/> 247 <tool file="mothur/deunique.tree.xml"/>
235 <tool file="mothur/TreeVector.xml"/> 248 <tool file="mothur/TreeVector.xml"/>
236 </section> <!-- metagenomics_mothur --> 249 </section> <!-- metagenomics_mothur -->
237 250
238
239 ############ DESIGN NOTES ######################################################################################################### 251 ############ DESIGN NOTES #########################################################################################################
240 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py 252 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
253
254 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
241 255
242 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name. 256 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
243 * Every tool will produce the logfile of the mothur run as an output. 257 * Every tool will produce the logfile of the mothur run as an output.
244 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py 258 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
245 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs 259 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs