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More automation for usegalaxy.* import #281

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lldelisle opened this issue Nov 14, 2023 · 2 comments
Open

More automation for usegalaxy.* import #281

lldelisle opened this issue Nov 14, 2023 · 2 comments

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@lldelisle
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If someone has time to do this it would be so cool...
In the log of the github action which install workflows on usegalaxy.* there are some important lines:

# usegalaxy.org
ERROR:root:Error importing #workflow/github.com/iwc-workflows/fragment-based-docking-scoring/main:v0.1.4 with message Imported, but some steps in this workflow have validation errors. 
ERROR:root:Error importing #workflow/github.com/iwc-workflows/fragment-based-docking-scoring/main:v0.1.2 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/fragment-based-docking-scoring/main:v0.1.1 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler:v0.3 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler:v0.3 with message Imported, but some steps in this workflow have validation errors. 
ERROR:root:Error importing #workflow/github.com/iwc-workflows/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler:v0.3 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/pox-virus-amplicon/main:v0.1 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/openms-metaprosip/main:v0.1 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/sra-manifest-to-concatenated-fastqs/main:v0.2 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/sra-manifest-to-concatenated-fastqs/main:v0.1 with message Imported, but some steps in this workflow have validation errors.

## EU
ERROR:root:Error importing #workflow/github.com/iwc-workflows/parallel-accession-download/main:v0.1.5 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/fragment-based-docking-scoring/main:v0.1.4 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/fragment-based-docking-scoring/main:v0.1.2 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/fragment-based-docking-scoring/main:v0.1.1 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler:v0.3 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler:v0.3 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler:v0.3 with message Imported, but some steps in this workflow have validation errors.
ERROR:root:Error importing #workflow/github.com/iwc-workflows/sra-manifest-to-concatenated-fastqs/main:v0.2 with message Imported, but some steps in this workflow have validation errors.

## AU TODO

Probably because:

  • Some tool versions are not present in the usegalaxy.*
  • Some tools are not present in the usegalaxy.*

What would be marvelous would be that a CI capture these lines, and write a PR to:

@lldelisle
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Alternatively, part of CI there should be the generation of the yaml like in GTN but it would be super nice to have the tool_panel_section_label updated.... Maybe this should go to planemo, no?

@lldelisle
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