search

bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
65 stars 17 forks source link

Using bcbio_setup_genome.py with bcbio-nextgen-vm? #149

Closed tomsing1 closed 8 years ago

tomsing1 commented 8 years ago

I have installed bcbio-nexten-vm following the steps outlined on the bcbio-nextgen-vm landing page. Before I can launch an analysis via bcbio_vm.py run I need to add a custom genome.

Is it possible to build the genome indices with this setup, e.g. given that the tools are within the bcbio/bcbio docker container?

Perhaps there is a way to run the bcbio_setup_genome.py command somehow? Thanks a lot for any ideas!

chapmanb commented 8 years ago

Thomas; Unfortunately, we don't currently have a way to run this script inside the Docker container, but it is included with the bcbio_vm distribution in:

/path/to/bcbio/anaconda/bin/bcbio_setup_genome.py

It should have all Python dependencies installed but not necessarily the external tools it called. But we haven't yet tested it with this setup so I'm not sure how well it will work. We will definitely migrate this functionality but likely as part of our new effort to support the Common Workflow Language with Docker (http://bcbio-nextgen.readthedocs.org/en/latest/contents/cwl.html).

Is installing standard bcbio_nextgen.py an option now if you need to add in custom genomes?

Hope this helps.

tomsing1 commented 8 years ago

Thank you for your quick response and for pointing out the location of the bcbio_setup_genome.py script. Unfortunately, it doesn't seem to run without external tools (e.g. picard).

I will go ahead and install the standard bcbio_nextgen.py as you recommended and am looking forward to CWL options you guys are working on!

fgvieira commented 4 years ago

@chapmanb Has this issue been fixed? I mean, is it possible to add a custom genome to bcbio-vm? thanks,