FW: ShortBRED

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Levesque, Nicole M.

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Nov 14, 2019, 2:15:46 PM11/14/19
to shortbr...@googlegroups.com

 

 

From: Joan Slonczewski <slonc...@kenyon.edu>
Sent: Monday, November 11, 2019 4:12 PM
To: Huttenhower, Curtis <chut...@hsph.harvard.edu>
Cc: Daniel Barich <bar...@kenyon.edu>; Levesque, Nicole M. <leve...@hsph.harvard.edu>
Subject: ShortBRED

 

Curtis,

I just sent a message (below) to the ShortBRED user group, but it bounced.

Please let me know if we need to do anything else to check our questions on installation, or if an updated installation source is available.

Thanks very much,

Joan

 

Subject: ShortBRED help installing
To: shortbr...@googlegroups.com

 

Could you please let us both join the ShortBRED group, and assist with installation on our workstation.
Question: Do all the "dependencies" need to be installed individually first before your ShortBRED?
What if some "dependency" versions are outdated?
These are the versions listed on your site:
Python 2.7.9
Biopython v1.65
ncbi-blast-2.2.28+
usearch v6.0.307 (Please make sure this is up to date. Earlier versions of usearch use a different command for making database than what is expected by ShortBRED.)
MUSCLE v3.8.31
CD-HIT version 4.6

Thanks for your help,

Joan L. Slonczewski
Professor of Biology
Higley Hall, 202 N. College Road
Kenyon College
Gambier, OH 43022
http://biology.kenyon.edu/slonc/slonc.htm
slonc...@kenyon.edu
Phone: 740-427-5397
Text: 740-504-2215

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