Fix tools writing to Galaxy's files directory

[bernt-matthias]

With galaxyproject/planemo#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 #3986 (comment)

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 barrnap avoid writing to inputdir #4104
• commet .dat_multi_k31_s4.h5
• crossmap_* .dat.fai .unmap Symlink crossmap_vcf fasta input to prevent writing to the input directory to generate fasta index #4126
• delly_* .dat.fai
• discosnp_pp .dat_multi_k31_s4.h5
• fermikit fermikit: avoid writing to inputdir #4105
  • fermi2 .dat.fai
  • fermikit_variants .dat.fai
• hyphy_* .dat.fit.bf
• irissv .dat.bai Irissv: fix errors related to bai file creation #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 ... tetyper: avoid writing indices to inputdir #4107
• tradis_* .dat.bwt .. Bio-TraDis: avoid writing to input directory #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?

[bernt-matthias]

This should now be covered by the containerized tool tests.