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test-data
tool-data
.shed.yml
README
align.check.xml
align.seqs.xml
amova.xml
anosim.xml
bin.seqs.xml
biom.info.xml
chimera.bellerophon.xml
chimera.ccode.xml
chimera.check.xml
chimera.perseus.xml
chimera.pintail.xml
chimera.slayer.xml
chimera.uchime.xml
chimera.vsearch.xml
chop.seqs.xml
classify.otu.xml
classify.seqs.xml
classify.tree.xml
clearcut.xml
cluster.classic.xml
cluster.fragments.xml
cluster.split.xml
cluster.xml
collect.shared.xml
collect.single.xml
consensus.seqs.xml
cooccurrence.xml
corr.axes.xml
count.groups.xml
count.seqs.xml
create.database.xml
degap.seqs.xml
deunique.seqs.xml
deunique.tree.xml
dist.seqs.xml
dist.shared.xml
fastq.info.xml
filter.seqs.xml
filter.shared.xml
get.communitytype.xml
get.coremicrobiome.xml
get.dists.xml
get.group.xml
get.groups.xml
get.label.xml
get.lineage.xml
get.mimarkspackage.xml
get.otulabels.xml
get.otulist.xml
get.oturep.xml
get.otus.xml
get.rabund.xml
get.relabund.xml
get.sabund.xml
get.seqs.xml
get.sharedseqs.xml
heatmap.bin.xml
heatmap.sim.xml
homova.xml
indicator.xml
lefse.xml
libshuff.xml
list.otulabels.xml
list.seqs.xml
macros.xml
make.biom.xml
make.contigs.xml
make.design.xml
make.fastq.xml
make.group.xml
make.lefse.xml
make.lookup.xml
make.shared.xml
make.sra.xml
mantel.xml
merge.count.xml
merge.files.xml
merge.groups.xml
merge.sfffiles.xml
merge.taxsummary.xml
metastats.xml
mimarks.attributes.xml
nmds.xml
normalize.shared.xml
otu.association.xml
otu.hierarchy.xml
pairwise.seqs.xml
parse.list.xml
parsimony.xml
pca.xml
pcoa.xml
pcr.seqs.xml
phylo.diversity.xml
phylotype.xml
pre.cluster.xml
primer.design.xml
rarefaction.shared.xml
rarefaction.single.xml
remove.dists.xml
remove.groups.xml
remove.lineage.xml
remove.otulabels.xml
remove.otus.xml
remove.rare.xml
remove.seqs.xml
rename.seqs.xml
reverse.seqs.xml
screen.seqs.xml
sens.spec.xml
seq.error.xml
sffinfo.xml
shhh.flows.xml
shhh.seqs.xml
sort.seqs.xml
split.abund.xml
split.groups.xml
sub.sample.xml
summary.qual.xml
summary.seqs.xml
summary.shared.xml
summary.single.xml
summary.tax.xml
taxonomy-to-krona.xml
tool_data_table_conf.xml.sample
tools.yaml
tree.shared.xml
trim.flows.xml
trim.seqs.xml
unifrac.unweighted.xml
unifrac.weighted.xml
unique.seqs.xml
venn.xml

README

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
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