review the toolset to identify pulsar incompatibility

[martenson]

some tools we provide are not pulsar compatible, we should remove them or fix them

[zsalvet]

What makes them incompatible with pulsar? Is it valid in general or works due to luck only with local runner ?

[martindemko]

Do you mean builtin tools or some tools from shedtool too? Could you add few examples @martenson , please?

[martenson]

You guys are quick :).

• This is an example of expecting galaxy code (this could be treated by altering the image it defaults to to include it)

• This is an example of tools that do not properly define their scripts: pulsarify all tools in the repo workflow4metabolomics/tools-metabolomics#281
• This is an example of broken requirements somewhere half way switch shipped export_remote tool to proper dependencies galaxyproject/galaxy#19675

There are likely other types not included here.

[martindemko]

Thanks @martenson. It looks like some are already on the way to be fixed, but anyway, I vote for removing those that nobody ever used on GCZ and let the worries for later or for somebody who needs these tools.

[martenson]

GCZ has a low overall usage, I believe we shouldn't base our decision on that statistics. Nevertheless a review is warrantied I think. We can find inspiration in usegalaxy Australia, that uses Pulsar exclusively afaik