tools-iuc
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Fix tools writing to Galaxy's files directory
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.
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.
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?
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?