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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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missing dependencies on custom install? #14

Closed accopeland closed 9 years ago

accopeland commented 9 years ago

Hi,

I was forced to do a custom install which seemed to complete without error. Subsequently tried to run checkm --help and traceback indicated ScreamingBackpack was not found. I installed this into my local python lib directory then retried. Next traceback indicated dendropy was not found. After installing dendropy into my custom python lib directory, checkm runs fine. I see the ScreamingBackpack requirement in setup.py so I am not sure how/why this happened.

Also, I found that hmmer/3.1b1 is needed since hmmer/3.0 does not read the checkm hmm files correctly, or so checkm reports.

ctSkennerton commented 9 years ago

Hi Alex,

This isn't really an issue with checkM but instead is an issue with python packaging (one of the many). When you run python setup.py it doesn't actually check that any of the dependancies are installed. Using a python package manager like pip does give you this functionality.

accopeland commented 9 years ago

OK, thanks.

On Thu, Nov 13, 2014 at 2:09 PM, Connor T. Skennerton < notifications@github.com> wrote:

Hi Alex,

This isn't really an issue with checkM but instead is an issue with python packaging (one of the many). When you run python setup.py it doesn't actually check that any of the dependancies are installed. Using a python package manager like pip does give you this functionality.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/CheckM/issues/14#issuecomment-62975732.

Alex Copeland Joint Genome Institute, Walnut Creek, CA 94598