File not found: /bbx/input/biobox.yaml

[richardgoater]

Doesn't matter what command is provided, the above is all the output I can get. Applies for both locally-built images and the image on docker hub. Any thoughts?

[michaelbarton]

Hi @richardgoater, this shovill image uses the biobox interface. We "hope" this simplifies running bioinformatics software because all software of the same type has the same interface. There's documentation here:

http://bioboxes.org/docs/assemble-a-genome/

In short, after you have installed the bioboxes python interface you can use the command:

biobox run \
  short_read_assembler \
  bioboxes/shovill \
  --input reads.fq.gz \
  --output contigs.fa

If you're not too keen on using this, you can still use the base image by overriding the entrypoint in the image using the docker --entrypoint command.

cc @tseemann

[richardgoater]

Hi Michael, thanks very much for the tip.

On Thu, 19 Oct 2017 at 17:58 Michael Barton notifications@github.com wrote:

Hi @richardgoater https://github.com/richardgoater, this shovill image uses the biobox interface. We "hope" this simplifies running bioinformatics software because all software of the same time has the same interface. There's documentation here:

http://bioboxes.org/docs/assemble-a-genome/

In short, after you have installed the bioboxes python interface you can use the command:

biobox run \ short_read_assembler \ bioboxes/shovill \ --input reads.fq.gz \ --output contigs.fa

If you're not too keen on using this, you can still use the base image by overriding the entrypoint in the image using the docker --entrypoint command.

cc @torstenseeman

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bioboxes/shovill/issues/5#issuecomment-337971306, or mute the thread https://github.com/notifications/unsubscribe-auth/ABXQ2TrZnHbH_VA5B2D3C9doErsniT_fks5st3-sgaJpZM4P_Esw .

[michaelbarton]

Thanks Richard.