M Bernt
**Describe the bug** For this request ``` pysradb search --db sra --query 'NextSeq 500 stress' --source 'transcriptomic' --organism 'Arabidopsis thaliana' --platform 'illumina' --selection 'random' --strategy 'rna seq' --max 20 --verbosity...
**Describe the bug** A command lacking the `--publication-date` argument like ``` pysradb search --db sra --query 'cancer' --source 'transcriptomic' --organism 'Homo sapiens' --platform 'illumina' --max 100 --verbosity 2 --stats --graphs...
Wondering if it would be possible/useful to annotate OpenMS tools (and formats) with terms from an ontology like - http://edamontology.org - https://www.psidev.info/groups/controlled-vocabularies Currently "only" the whole tool suite seems to...
testing - `-out_spec`, `-out_topFD`, `-out_topFD_feature` - mzML with MS2 only, and MS1-3 Is there nowadays a way to test the written tsv file contents .. and maybe check if certain...
While working on new Galaxy tools I stumbled over the following errors when executing the OpenMS tests in a fresh conda environment ``` ../prepare_test_data.sh: line 54: 887733 Aborted (core dumped)...
When executing the test `TOPP_SiriusAdapter_1` (and many others using sirius) in a conda environment I get the following: ``` stderr: Error: Unexpected internal error (Sirius was executed, but an empty...
When executing the OpenMS tests (during Galaxy tool development) I get: ``` executing TOPP_AssayGeneratorMetabo_8 ../prepare_test_data.sh: line 1878: 891951 Segmentation fault (core dumped) AssayGeneratorMetabo -test -sirius_executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML...
Would be cool if there would be a changelog, or if releases to pypi would be tag-ed here.
Otherwise [this](https://github.com/galaxyproject/planemo/blob/28b2ca40ceaa546b0b23678220e05bf155829ea7/planemo/autopygen/argument_parser_conversion.py#L103) error is just empty.