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hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
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Functional database installation #69

Closed ctSkennerton closed 7 years ago

ctSkennerton commented 9 years ago

I'm a little confused about downloading some of the functional databases. I downloaded the file MetaPathwaysDBs.zip which contains the cog and metacyc databases. In the wiki though under the section "Installing Reference Databases" there are also links to the COGs ftp site and the metacyc website. Are these different databases that I need to install, aside from the ones included in the zip archive?

more questions:

  1. the refseq database comes in multiple parts, do I need to concatenate them all into one file for use in metapathways?
  2. Is it possible to get the KEGG database from 2011, is it hosted somewhere?
  3. There is a link under the Carbohydrate-Active enZYmes (CAZy) database that talks about a specialized version for metapathways, however the link just points back to the wiki page
taltman commented 8 years ago

::Bump::

ariahahn commented 8 years ago

Hi Connor,

Any database can be used and you dont need to use all of them. So it's not necessary to have a specific set of databases. Note that metacyc is recommended if you wish to build epgdbs. Yes each database needs to be in a single fasta file (including refseq). Start with the archive and see which additional databases you'd like. the Kegg database is hosted by Kegg and by googling Kegg database many resources and citations will come up. Let me know how far you get and I'll do my best to help you get what you need. I may be able to create new links for you to access some databases if they are not in the archive. Let me know specifically which databases these would be and I'll see if I have a copy. On 10 Apr 2015 2:24 pm, "Connor T. Skennerton" notifications@github.com wrote:

I'm a little confused about downloading some of the functional databases. I downloaded the file MetaPathwaysDBs.zip which contains the cog and metacyc databases. In the wiki though under the section "Installing Reference Databases" there are also links to the COGs ftp site and the metacyc website. Are these different databases that I need to install, aside from the ones included in the zip archive?

more questions:

  1. the refseq database comes in multiple parts, do I need to concatenate them all into one file for use in metapathways?
  2. Is it possible to get the KEGG database from 2011, is it hosted somewhere?
  3. There is a link under the Carbohydrate-Active enZYmes (CAZy) database that talks about a specialized version for metapathways, however the link just points back to the wiki page

— Reply to this email directly or view it on GitHub https://github.com/hallamlab/metapathways2/issues/69.

taltman commented 8 years ago

I'm also eagerly awaiting the fixed CAZy database link. Thanks!

taltman commented 8 years ago

Ah, a working link to the CAZy database can be found on this page:

https://github.com/hallamlab/metapathways2/releases/tag/v2.5

MP team, can you please update the wiki page's link, now that I found it for you? :-p

taltman commented 8 years ago

Pro-tip: You can get a partial copy of the KEGG database from the HMP HMFUNC resource. Not sure if MetaPathways can use its formatted output for displaying pretty hierarchy reports, though...