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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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Troubles with a Docker implementation of iMetAMOS #275

Open aldembert opened 6 years ago

aldembert commented 6 years ago

Hi Sergey and metAMOSTeam!

We are working on putting together imetAMOS from the next Docker: https://hub.docker.com/r/ml642810/metamos/

We already found that we need to include the workflow in enabled.ini and that we need to install the extra packages required by iMetAMOS (like kmergenie) but do you have any suggestions to make this work faster?

Thanks in advance

Salvador Angel

skoren commented 6 years ago

I'm not sure what you are asking, you want the install to work faster? metAMOS will pick up most tools from the users path so if you already have the dependencies installed, you can run the provided INSTALL.py script to set everything up and then just package that result.

avrixtor commented 6 years ago

Do you guys have a metAMOS Docker image ready to run python INSTALL.py iMetAMOS? If not, we are working on it so that it works with as most functions as possible. So far we cannot get Test to work with -f Assemble,MapReads,Propagate,Abundance,Validate starting FROM ml642810/metamos:v1. It cannot even finish INSTALL.py iMetAMOS