Re: ShortBRED help installing

[Daniel Barich]

I tried installing shortbred via conda and docker, but neither one worked.  I couldn't figure out what was meant in the tutorial by 'update your channels before installing.'

On Mon, Nov 11, 2019 at 3:55 PM Joan Slonczewski <slonc...@kenyon.edu> wrote:

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What if some "dependency" versions are outdated?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

--

Daniel Barich

Barich Assistive Technology

Gambier, OH 43022

[Daniel Barich]

Ok, I just switched to a python2 environment in conda and the install worked.  I didn't realize the program wouldn't work with python 3.  Considering that python 2 is near end of life, the code should be updated to work with python 3.

Thanks.

Daniel

[Eric Franzosa]

Agreed Daniel and thanks for bringing this to our attention.

Thanks,

Eric

On Tue, Nov 12, 2019 at 9:48 AM Daniel Barich <bar...@kenyon.edu> wrote:

Ok, I just switched to a python2 environment in conda and the install worked.  I didn't realize the program wouldn't work with python 3.  Considering that python 2 is near end of life, the code should be updated to work with python 3.

Thanks.

Daniel

On Mon, Nov 11, 2019 at 4:25 PM Daniel Barich <bar...@kenyon.edu> wrote:

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