usegalaxy.fr covid workflow

[lecorguille]

We already have some published workflow based on the https://covid19.galaxyproject.org/ : https://usegalaxy.fr/workflows/list_published

I don't know if there are versionned but we should update them if needed and re-publish with another account.

We can set a gitlab repo to publish workflow through CI with the up-to-date version using bioblend?

It will be useful even if we create a dedicated separate Galaxy instance

[drosofff]

Yes @lecorguille , I suppose that it makes sense to do this to integrate information from this repo in the software infrastructure of usegalaxy.fr, which is indeed my view - to be discussed as necessary. However, I will also advocate for having this github repo alive, because my plan is clearly not to let it private. I think that @jvanheld mentioned this move in the last Emergen workflow meeting. There is 3 reasons for this:

• github has a larger user base in France and abroad, thus better findability
• there are many repo that will be useful for development and these are most often in GitHub. For instance see this one which is probably of first importance for automation with bioblend https://github.com/usegalaxy-eu/ena-cog-uk-wfs
• There is a value of staying in line with what as been done by the Galaxy community (usegalaxy.eu-org-au) for covid19 analyses, in terms or visibility. And most often (not to say always) this is available in a public GitHub repo.

[lecorguille]

I'm not saying that you should give up with this repo. But now, that you are mention it ... :P

• All our gitlab repos around usegalaxy.fr are in open access, you only need to be part of the team in order to launch jobs on our Galaxy instances
• GitLab isn't so bad indexed : https://www.google.com/search?q=usegalaxy.fr+git .
• Behind GitLab and GihHub, it's git so no limitation about that. About the CI, we can do almost the same things (even linking a jenkins if needed).
• Currently, at usegalaxy.fr we are using gitlab-runner. A CI technology that wasn't available in GitHub before the GitHub Actions.
• GitLab can have some advantages that you can't get if you never try. Like the subgroup https://gitlab.com/ifb-elixirfr/usegalaxy-fr/ that allow to organise the dev by thematics.

Finally, the choose is either split usegalaxy.fr dev or just have the same domain url github.com than partners.

[drosofff]

I am not sure if this issue is a big one or even if it is one. In term of visibility I was not speaking of Galaxy. Try covid19 + git, or sars-cov-2 + git or anything + git. In any case I am not a fan of the debate hub versus lab. If something is working, we'll not reinvent it and will use it. So no issue on this side imho.

More important is to structure a plan for covid19 analyses by the usegalaxy.fr galaxy infrastructure. We also need a chat channel and a trello board-like thing, with the possibility to invite galaxy community members for help or advices. I had extensive discussions with the Galaxy devteam over last week. I feel this is the moment for a conf call to kick off the project

[lecorguille]

Hop, GitLab provide a Trello-Board like experience: https://gitlab.com/groups/ifb-elixirfr/usegalaxy-fr/-/boards In case, I already create a label covid19 that will allow to filter easily during meetings or in order to share the board... in case.

We can also create a dedicate subgroup covid19 in https://gitlab.com/groups/ifb-elixirfr/usegalaxy-fr to have a place where we can put meetings Readme, CR, boards, issues, ... without real codes.

[drosofff]

@lecorguille there is already a covid group in this github organisation, we can create a dozen more if needed. The trello board experience also exists (https://github.com/IFB-ElixirFr/EMERGEN-workflows/projects) as well as all items you mentioned. Let's meet, lets's talk, let's count us. These are the highest priorities. Can you help me to focus a max of people on this repo, while avoiding cleaving on minor points ? We can move everywhere else after, if it is needed and/or justified.