Make an ARGOS Archive for data.argosdb

[cwoodside1278]

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]

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