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Add CLI command to get and put JBrowse config files in collaboration server #437

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merged 3 commits into from
Sep 19, 2024

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shashankbrgowda
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@shashankbrgowda shashankbrgowda commented Sep 9, 2024

Fixes #433, fixed #214

Example:

apollo-cli % yarn dev jbrowse get-config --profile apollo > config.json

apollo-cli % jbrowse add-track https://ftp.ebi.ac.uk/pub/databases/havana/ngs_havana/CLS/updated_master_table/human/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1.bam --indexFile https://ftp.ebi.ac.uk/pub/databases/havana/ngs_havana/CLS/updated_master_table/human/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1.bam.bai --assemblyNames=66bb60e83db15a4a2aff224d
Added track with name "pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1" and trackId "pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1" to ./config.json

apollo-cli % yarn dev jbrowse set-config --profile apollo config.json
Jbrowse configuartion added successfully to apollo

@garrettjstevens garrettjstevens marked this pull request as ready for review September 19, 2024 20:42
@garrettjstevens garrettjstevens merged commit 096c318 into GMOD:main Sep 19, 2024
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