Switch to IUC style CI

[bernt-matthias]

I just noted that there is no biocontainer for trimmomatic and thought that there should be. We could add this repo to planemo-monitor .. but for this, we should use state-of-the-art CI. Alternatively, we can move trimmomatic to IUC?

TODOs:

• add .shed.yaml for all tools that should be tested
• move all tools that are currently not tested to legacy?
• rename legacy to deprecated?
• add repo to https://github.com/galaxyproject/planemo-monitor for automatic container building

[pjbriggs]

Hello @bernt-matthias thanks for the PR & sorry not to respond earlier - I've just got back after a couple of weeks.

Can I just check my understanding of the aims of the PR? If I understand correctly then:

• The proposal is to add this repo (i.e. fls-bioinformatics-core/galaxy-tools) to planemo-monitor specifically in order to ensure testing of the trimmomatic tool. However as some (all?) of the other tools in the repository (which you not interested in?) are showing issues under planemo-monitor, a part of the proposal is to make certain modifications to the repo (outlined in the TODOs) so that planemo-monitor will skip testing of those tools.

• An alternative to the proposal would be to transfer the trimmomatic tool to the IUC tool repository.

Does this sound correct? Thanks

[bernt-matthias]

Jep

[bernt-matthias]

An alternative to the proposal would be to transfer the trimmomatic tool to the IUC tool repository.

How about just doing this first?

[pjbriggs]

Hello @bernt-matthias many apologies I have been meaning for some time to pick this up again but things have gotten away from me recently. Thanks for the reminder!

I did discuss this with my line manager and he was supportive of moving the Trimmomatic tool to the IUC repo, where I think it would be better cared for in future than I have been able to do over the past couple of years.

So if you think this is also a good idea then is it really just a case to begin with of making a PR on the https://github.com/galaxyproject/tools-iuc repo?

[bernt-matthias]

is it really just a case to begin with of making a PR on the https://github.com/galaxyproject/tools-iuc repo?

Nearly. I could do this is desired.

The only thing needed from your side would to give write permission on the TS for the iuc account.

[pjbriggs]

Thanks @bernt-matthias. I'm finishing now until the new year but I'm happy to start the PR when I get back. However if you'd like to begin before then that would also be okay with me.

[pjbriggs]

@bernt-matthias happy new year! I've kicked off a new issue #91in this repo and started a branch in my fork of the IUC tools repo, but I haven't yet made a PR as there are a few things I'm unsure about - I'll add these to issue #91 next.

[pjbriggs]

Closing as PR has been superseded as Trimmomatic tool has now been relocated to the IUC tools repo (see issue #91 for details).