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bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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Docker classification issue: #20

Closed EisenRa closed 7 years ago

EisenRa commented 7 years ago

Dear authors,

Thank you for making this great software!

I'm having an issue running MATAM through docker, it works fine until the classification step, then outputs this error:

INFO - Write abundance informations to: /matam/matam_assembly/scaffolds.NR.min_500bp.fa.abd INFO - === Taxonomic assignment === No valid binary found for classifier

Seems like it's not finding the rdp binaries?

Any help would be greatly appreciated.

Best regards, Raphael

ppericard commented 7 years ago

Yes, you're right, we didn't update the Dockerfile with the last build. We'll correct that asap. By curiosity, since you're the first user to use MATAM through docker, what guided your choice of distribution mode ? We tend to encourage our user to get MATAM with conda since it is easier to install and use, but it doesn't run on all operating systems.

ppericard commented 7 years ago

@loic-couderc : we need to check the dependencies installed on the ubuntu image. We need to add at least ant.

loic-couderc commented 7 years ago

Dear @EisenRa,

I have updated the docker image to take into account your issue. You can download the new image:

docker pull bonsaiteam/matam

Then, to avoid to run all MATAM's steps again, you can add the flag --resume_from abundance_calculation to your command line with the same parameters.

EisenRa commented 7 years ago

Dear Pierre,

Thank you for the quick response!

I've just tried installing it and running it through conda on our linux server -- works fine!

The reason that I started with docker was that my work machine is a Mac, and I've historically had issues installing dependencies etc. on the server due to permissions. Though it appears that conda worked fine!

Much appreciated, Raphael