Fix tools writing to Galaxy's files directory

[bernt-matthias]

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With https://github.com/galaxyproject/planemo/pull/1190 its possible to detect tools that write to Galaxy's files directory. I'm running this on IUC here: https://github.com/bernt-matthias/tools-iuc/runs/3721212988?check_suite_focus=true

See also discussion in https://github.com/galaxyproject/tools-iuc/pull/3986#issuecomment-926729276

Here is a list of tools (from an earlier run of the CI workflow) that create at least one extra file:

• [ ] emboss .dat.1.png
• [ ] bacteria_tradis .dat.bwt ...
• [ ] barrnap .dat.fai https://github.com/galaxyproject/tools-iuc/pull/4104
• [ ] commet .dat_multi_k31_s4.h5
• [ ] crossmap_* .dat.fai .unmap https://github.com/galaxyproject/tools-iuc/pull/4126
• [ ] delly_* .dat.fai
• [ ] discosnp_pp .dat_multi_k31_s4.h5
• [ ] fermikit https://github.com/galaxyproject/tools-iuc/pull/4105
  • fermi2 .dat.fai
  • fermikit_variants .dat.fai
• [ ] hyphy_* .dat.fit.bf
• [ ] irissv .dat.bai https://github.com/galaxyproject/tools-iuc/pull/4642 1.0.4+galaxy2
• [ ] kissplice .dat_multi_k31_s4.h5
• [ ] lordec .dat_multi_k31_s4.h5
• [ ] mapsembler2 .dat_multi_k31_s4.h5
• [ ] medaka_* .dat.fai ...
• [ ] nanocompore_* .dat.fai
• [ ] picard_* .dat.bai
• [ ] progressivemauve .dat.backbone
• [ ] pyega3 .dat.md5
• [ ] stringtie* .dat.bak
• [ ] takeabreak .dat_multi_k31_s4.h5
• [ ] tetyper .dat.nto ... https://github.com/galaxyproject/tools-iuc/pull/4107
• [ ] tradis_* .dat.bwt .. https://github.com/galaxyproject/tools-iuc/pull/4103
• [ ] xmfa2gff3 .dat.backbone

I hope that the PR is accepted soon. Then it will also run for PRs.

Put your name / PR number next to the entries if you are working on one of the tools above.

[natefoo]

Thanks for assembling the list @bernt-matthias, this is fantastic! It'd be great if we could also record version numbers where this was fixed, which will make admins' lives much easier.

[bernt-matthias]

It'd be great if we could also record version numbers where this was fixed, which will make admins' lives much easier.

Any suggestion how to achieve this? Just a txt file, maybe in a gist?

[natefoo]

Yeah, I don't have a strong preference - gist, or just edit your comment in this issue to record it next to the tool ID as it is checked off?