avoid bam2msa to create BAM index in inputdir

[pavanvidem]

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[bernt-matthias]

Hey @pavanvidem .. how do you identify tools writing to the input dir?

[pavanvidem]

First, we extracted the dataset names from input dir that do not end with .dat using something like find . -not -name "*.dat" -type f | grep -v 'dataset_.*_files'. Then we used gxadmin query q to query the job table using each dataset name and extracted the tools out of it. Finally, we manually check/run each tool and fix it.

[bernt-matthias]

@pavanvidem I started some discussion here: galaxyproject/planemo#1189

[bernt-matthias]

Still the manual approach will be needed (since I guess we won't have perfect test coverage)...

[bernt-matthias]

Galaxy already stores the index files (only for bam) and you can access it with:$input.metadata.bam_index. So ln -s '$input.metadata.bam_index' input_bam.bai may avoid that bam2msa needs to recreate it?

But I guess then we need a version bump.

[bernt-matthias]

First, we extracted the dataset names from input dir that do not end with .dat using something like find . -not -name "*.dat" -type f | grep -v 'dataset_.*_files'. Then we used gxadmin query q to query the job table using each dataset name and extracted the tools out of it. Finally, we manually check/run each tool and fix it.

Hey @pavanvidem just thought a bit more about this. The problem is that old versions of the tool will still write to Galaxy's file dir. How about configuring your galaxy to run jobs as a separate user that does not have write permissions for Galaxy's file dir:

https://github.com/galaxyproject/galaxy/blob/40ddc72f485ae233f3a4aed63847ccb041003320/lib/galaxy/config/sample/galaxy.yml.sample#L2121

Still the problem needs to be fixed: I' currently running IUC's weekly CI with an extended version of planemo (galaxyproject/planemo#1190) : https://github.com/bernt-matthias/tools-iuc/actions/runs/1277704614

[pavanvidem]

Hey @pavanvidem just thought a bit more about this. The problem is that old versions of the tool will still write to Galaxy's file dir. How about configuring your galaxy to run jobs as a separate user that does not have write permissions for Galaxy's file dir:

This is a good idea. I should have mentioned that I queried the EU Galaxy database, not my local instance. This might have covered most of the old tool versions and the tools outside IUC.

[natefoo]

Your excellent work was foiled by the tool again @pavanvidem. It looks like this one generates the index regardless of whether it exists. If it's a symlink to a read-only file, then that fails.

I can generate a PR upstream, but for current versions of the tool I think we will have to remove the bai symlink and let the tool generate the bai itself, unfortunately.

[natefoo]

Upstream PR: veg/BioExt#45

[bernt-matthias]

@pavanvidem can you check if a bump of the tool version to 0.20.4 fixes this?