FROGS on usegalaxy.eu?

[bgruening]

Hi all,

we had some requests to add FROGS to the European Galaxy server. I looked at the tools and they look mostly great. A few things would need to be fixed, e.g. some security issues and IUC best practices https://galaxy-iuc-standards.readthedocs.io/en/latest/

Would you be interested to work with us to resolve this? Thanks, Bjoern

[mariabernard]

Hi Björn,

We worked together with Cristóbal around a year ago to improve FROGS wrappers, many thanks again for all your advices and corrections. We are currently working on a new version of FROGS, and some wrappers will be changed (one will be removed). It's a good timing to also improve other things such as security. Nevertheless, our task force is quite reduced in this moment, and we would like to published the new release by the end of March.

Could you list the main points that we do no respect ? And we will do our best to take them into account.

Have a nice day

Maria

[abretaud]

Hi! Same concern about usegalaxy.fr, it is already installed, but we'd better have a more secure version I think the first step would be to ensure all wrappers are using single quotes in the command line: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#command-formatting Are you working on the next version in a public branch?

[mariabernard]

Hi Anthony,

Yes we are working on public branch. If you and everyone else want to contribute, could you/them work on the dev branch ?

Indeed ,we have "Actions workflow" programed to be launched each time the master branch is modified. It's quite long as all tools are in one folder and could be annoying when multiple bu simple corrections are made.

When the FROGS 4.1.0 release will be available, I will merge the dev to the master branch from time to time of when someone ask to launched the workflow.

Thanks for the advice, we will take it into account.

Maria

[vindarbot]

Hello @bgruening

I try to launch planemo-ci actions from github , as follows :

https://github.com/geraldinepascal/FROGS-wrappers/actions/runs/4952537002/jobs/8858971902

And even though the first step (setup cache and determined changed repositories) is well done, the following steps remained on "skipped" statues

Do you know how to avoid this to achieve the whole workflow?

Thank you,

Vincent

[bgruening]

You need to touch a tool. The CI is only testing and pushing tools that have been changed.

[vindarbot]

Hi @bgruening @abretaud ,

We followed your recommendation to use single quotes in the command lines. Do you have any other recommendations for the tools to be "IUC compliant" prior to release?

Thanks in advance

[bgruening]

I think they look mostly good. I would recommend to run all tools once through https://github.com/galaxyproject/galaxy-language-server to reformat the XML a bit and maybe catch some linting issues. I can then review your PR if you like.

Thanks!

[vindarbot]

@bgruening I think this is good for the PR, I have some linting errors on the parameters related to the data tables, for example:

ERROR: Test 1: Test param category.value not found in the inputs

But to retrieve these parameters, this is the solution I found ... and the planemo tests are well executed.

Another thing, when I try to update the toolshed repo on testtoolshed galaxy, I get an error due to the size limit configured by the server. Since we have a lot of tools and test files, I guess I need to reduce the reference files before updating to toolshed.

Thank you for your help

[bgruening]

ERROR: Test 1: Test param category.value not found in the inputs

That sounds like a real problem. Maybe it does not yield to a tool test error but it seems you have a variable defined that is not necessary. Where is the PR, I can have a look if you like?

Another thing, when I try to update the toolshed repo on testtoolshed galaxy, I get an error due to the size limit configured by the server. Since we have a lot of tools and test files, I guess I need to reduce the reference files before updating to toolshed.

You can use tool suites. E.g. convert your https://github.com/geraldinepascal/FROGS-wrappers/blob/master/tools/frogs/.shed.yml to something similar to https://github.com/galaxyproject/tools-iuc/blob/f422a5a60caacffeeba4ce74a13d47aa96013e4e/tools/srst2/.shed.yml#L11

Changing this file will automatically split all tools into separate toolshed repos, which is the recommended way to update and deploy tools.

[vindarbot]

@bgruening Ok i will check the .shed.yml modification.

I have opened up a PR