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- [ ] tool_id toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0
- [ ] toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-mpa-report/1.2.4
Braken pulls in Kraken indexes, bu…
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### Description of the bug
Hey!
I was running the nascent pipeline v2.1.1 (v2.2.0 didn't work due to #) for two runs of the same sample.
I encountered an error at the step of `samtools sort`:
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Git, GitHub and others have been working on supporting the rename of the default branch of repositories from `master`. Most agreed with a new default of `main`.
References:
- Initial announcement …
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The latest Galaxy version comes with some nice assertions for imaging data: https://docs.galaxyproject.org/en/latest/dev/schema.html#assertions-for-image-data
When we update our instances/CI to Gal…
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``` pytb
galaxy.jobs.runners.pulsar ERROR 2016-05-20 12:54:43,326 failure finishing job 544006
Traceback (most recent call last):
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/p…
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The --augustus_species parameter in Funannotate appears to be for reusing Augustus training sets from previous runs of Funannotate. I'm not sure if this data is kept from one run to the next (the comm…
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Hi TeSS team,
I recently deployed a very wrong if/else case to my json-ld which added incorrect `mentions` to my materials. E.g. https://tess.elixir-europe.org/materials/marine-omics-identifying-bi…
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To support manually bumping a tool and not having to remember to reset it to `@VERSION_SUFFIX@`. See https://github.com/galaxyproject/tools-iuc/pull/6154#discussion_r1679181293
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When trying MaAsLin 2 I found some issues, that make the wrapper basically unusable.
(a) The fixed_effects can be different for every dataset, they are however hard-coded to only allow a choice of t…
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This would bring docker-galaxy-stable closer inline with planemo-machine.