Does Bpipe support Docker/Singularity container technology or Conda environments ?

[Neulhyo]

Hello,

Everything is in the question title : Does Bpipe support Docker/Singularity container technology or Conda environments ?

I have not seen anything about in it the documentation or in Q/A so I'm unsure about it. There is a paper about Nextflow (Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. doi:10.1038/nbt.3820) assuming that Bpipe does not support Docker containers but since I have seen that Bpipe does now support AWS and GCS cloud computing and storage, I've thought that the information about Docker may be out to date. 

Thank you in advance !

[Simon Sadedin]

Hi Neulhyo,

Bpipe doesn't currently provide any specific support for running commands or pipelines in containers.

Of course, it doesn't stop you at all from doing that if docker is available in your environment. But you have to, of course, provision (or build) the container image yourself, and then prefix your commands with the appropriate "docker run" and volume mounts so that the files are visible and mapped to the right locations etc.

I'd be curious to know what the kinds of features would be useful in this space - potentially it will not require too much work to add them and I can see it will be very generally useful to do so.

Cheers,

Simon

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