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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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A problem with initializing databases - code 255 #118

Closed blooria closed 1 year ago

blooria commented 2 years ago

I am having problems running mob_suite installed with: % git clone https://github.com/phac-nml/mob-suite.git % cd mob-suite % python setup.py install

I get a error code 255 Please help me fix this. Thank you

jrober84 commented 2 years ago

Hello,

please try installing using conda as there are other external programs you will need to have installed as well.

% conda config --add channels defaults % conda config --add channels conda-forge % conda config --add channels bioconda % conda install -c bioconda mob_suite

kbessonov1984 commented 2 years ago

Hello,

Code 255 usually means that remote server is down. Perhaps our database hosting at zenodo.org was down at the time you tried to install the tool?

I was not able to reproduce your error in a Docker container by cloning the master branch source code and running install on a fresh Ubuntu 20.04. In my case all dependencies and databases initialize with no errors.

To help you with the install from the source code, the Dockerfile is available at mob_suite/docker/Dockerfile. It allows to build a local image of a tool and has all step by step commands to install locally. Due to large ete3 library taxonomy dependency, mob_init takes awhile to initialize. As an option you can save time and pull Docker and Singularity images with initialized database available from https://biocontainers.pro/tools/mob_suite and https://hub.docker.com/r/kbessonov/mob_suite

jrober84 commented 1 year ago

I am marking this as closed for now