Where communities thrive

Join over 1.5M+ people
Join over 100K+ communities
Free without limits
Create your own community

Explore more communities

bioboxes/rfc

Request for comments on interchangeable bioinformatics containers

People

Repo info

Activity

Paolo Di Tommaso

@pditommaso

why don't you use command line parameters?

Michael Barton

@michaelbarton

because if you are specifying multiple fasta files with different insert sizes it quickly becomes just as difficult.

The issue is #61

It was the longest discussion we had.

I would be happy to read a proposal for a simpler interface, however I would ask that you read that discussion first.

Paolo Di Tommaso

@pditommaso

ok, now that you pointed out the issue I will read that thanks

Michael Barton

@michaelbarton

Thanks. We do welcome input from everyone. I know you have a lot experience from nextflow.io, so I would be glad to read any feedback or suggestions you have.

Paolo Di Tommaso

@pditommaso

surely

ah, I think there's a typo in at this page

http://bioboxes.org/guide/developer/build-your-image/

using the BASE directive

should not be:

using the FROM directive

Michael Barton

@michaelbarton

Thanks for spotting that - bioboxes/bioboxes.org#35

If you have any suggestions for the website, we welcome those too.

A PR ekcetera ..., everything is up for discussion.

I hope this standard will be developed by the community rather than only by me and @pbelmann.

Paolo Di Tommaso

@pditommaso

it looks nice, I would make just larger and with a bigger font

Michael Barton

@michaelbarton

The font is difficult to read?

Paolo Di Tommaso

@pditommaso

not difficult, but there's a lot of empty space

a bigger font would be more confortable

Michael Barton

@michaelbarton

If you refresh that page, it should say FROM now.

Paolo Di Tommaso

@pditommaso

yep!

btw, are you coming to Docker symposium at King's College, aren't you ?

Michael Barton

@michaelbarton

I hope so. I have to work it out with the JGI so that I will be allowed to attend.

Paolo Di Tommaso

@pditommaso

I see, hope to see you there if so

Michael Barton

@michaelbarton

Yes, it would be good to meet you in person.

I would like to meet everyone in the bioinformatics community who has been experimenting with Docker too.

Michael Barton

@michaelbarton

This looks great @pbelmann. Thanks for fixing the problem.

pbelmann

@pbelmann

Michael can we merge bioboxes/validator-short-read-assembler#27 ,so the validator works with the new file-validator?

Michael Barton

@michaelbarton

I’ll start a rebuild on the CI server - https://circleci.com/gh/bioboxes/validator-short-read-assembler/110

pbelmann

@pbelmann

great. Sorry for the merge conflicts.

Michael Barton

@michaelbarton

No problem. That PR was very useful.

It looks like there some lxc-start problems on circleci

I’ll clear the cache and rebuild, I think the previous build of velvet with the old file validator is included.

pbelmann

@pbelmann

Michael Barton

@michaelbarton

https://circleci.com/gh/bioboxes/validator-short-read-assembler/111

pbelmann

@pbelmann

nice

so it was the cache?

Michael Barton

@michaelbarton

The problem is here - https://github.com/bioboxes/velvet/blob/master/Dockerfile#L24

Yes

Because Docker thinks that the images are identical because the Dockerfiles are the same.

Therefore it uses the existing image without rebuilding.

This may or may not be an issue in future.

We can keep it in mind, I don’t think we need to do anything about it now.

pbelmann

@pbelmann

I agree

Michael Barton

@michaelbarton

Thanks again for solving this, switching out both nuitka and validictory was a very good solution.

pbelmann

@pbelmann

Thanks but it was a few hours work

I noticed it when I was working on the new binning spec