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Make an ARGOS Archive for data.argosdb #535

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cwoodside1278 opened this issue Mar 14, 2025 · 1 comment
Open

Make an ARGOS Archive for data.argosdb #535

cwoodside1278 opened this issue Mar 14, 2025 · 1 comment
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ARGOS Paper Anything pertaining to the paper directly Data Push new item/item needed for a successful data push Enhancement New feature or request

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@cwoodside1278
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Raja wants some of the tables archived but still accessible on data.argosdb. What he wants to create is
https://data.argosdb.org/archive where all of the files that we have listed in this decision tree doc will get moved to.
So those archived tables will not be seen on the homepage for data.argosdb.org

@cwoodside1278 cwoodside1278 added Enhancement New feature or request Data Push new item/item needed for a successful data push ARGOS Paper Anything pertaining to the paper directly labels Mar 14, 2025
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Deciding which ARGOS tables need to be archived.


Table Name Christie’s Decision Raja’s Decision
ngsQC_NCBI.tsv 50/50, because the table in the DB does not contain them all, but the physical table in the Google Drive contains everything. Decide if we want to push the full one or just archive Update with full data and push
biosampleMeta_NCBI.tsv 50/50, “” Update with full data and push
assemblyQC_NCBI.tsv 50/50, “” Update with full data and push
siteQC_HIVE.tsv Archive. Uses HIVE2 and we no longer perform siteQC Archive
assemblyQC_HIVE.tsv Archive. Old schema and was from HIVE2 QC. Also not positive it is all the assemblies from the BioProject Archive
ngsQC_HIVE.tsv Archive, “” Archive
biosampleMeta_HIVE.tsv Archive, “” Archive
property_definition.tsv Keep, but update Keep, but update
core_property_list.tsv Keep, but update Keep, but update
annotation_property_list.tsv Keep, doesn’t need to be updated Keep, and review. Might need update for paper
ngs_id_list.tsv 50/50, explains why you all chose those extra organisms, but also that can be listed on the wiki and not here? Move to wiki
DRM_all_orgs.tsv Archive. Not sure if it is applicable anymore archive
assemblyQC_HIVE3.tsv Archive. It is repetitive for “_ARGOS” and “_ARGOS_unreviewed” archive
ngsQC_HIVE3.tsv Archive. “” archive
biosampleMeta_HIVE3.tsv Archive. “” archive
NC_045512_SARS-CoV-2_Wuhan.fasta You said keep so keep Archive. This is present in NCBI
reference-guided_genome_assemblies_HIVE-Hexagon.fasta Archive. But I probably need to use this to re-check the marburg virus I ran Rename the file “generated_assembly_ARGOS_fastas”Give unique IDs to the Marburg FA10SRR17261988 and For SARS genomedelete itWe need to keep all the assemblies we are making.
reference-guided_genome_assemblies_Galaxy.fasta Archive. Not sure why we would need it archive
ngsQC_ARGOS    
assemblyQC_ARGOS    
biosampleMeta_ARGOS    
ngsQC_ARGOS_extended done  
assemblyQC_ARGOS_extended done  
biosampleMeta_ARGOS_extended done  
generated_assembly_ARGOS_fastas_extended March 13 - Have not made it yet make a ticket  

What does Archive mean


Put files here https://data.argosdb.org/archive Ask Jonathon to do this. Call Raja if it is not clear


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