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2020-11-13generation of dates a little more robustAndreaGuarracino
2020-11-13to not create YAML files with date before 2019 DecemberAndreaGuarracino
2020-11-13fix in the ids to considerAndreaGuarracino
2020-11-13added ids-to-consider option to the NCBI scriptAndreaGuarracino
2020-11-12managed the assembly_method in the scripts, doc, and the example templatesAndreaGuarracino
2020-11-12updated alignment_protocol field in the script, doc, and the example templatesAndreaGuarracino
2020-11-11Conflict in guix-deployPjotr Prins
2020-11-11DeploymentPjotr Prins
2020-11-11Move files to correct folderlltommy
2020-11-11Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-11-11Adding covid death and covid cases per country as additional background ↵lltommy
information
2020-11-11create_sra_metadata script doesn't trick the quality control about missing ↵AndreaGuarracino
date aymore
2020-11-10virtuoso: no-cachePjotr Prins
2020-11-10virtuoso: header changePjotr Prins
2020-11-10virtuoso: Added a --no-cache optionPjotr Prins
2020-11-08Uploaded UTHSC sequencesPjotr Prins
2020-11-08UTHSC samplesPjotr Prins
2020-11-06Add country entries that miss coordinatesPjotr Prins
2020-11-06Country trouble shootingPjotr Prins
2020-11-06CountriesPjotr Prins
2020-11-06Using correct wikidata geo linkPjotr Prins
2020-11-06Adding Tennessee itemsPjotr Prins
2020-11-06UTHSC upload infoPjotr Prins
2020-09-29esr_samples script refactoring; added a reference of the esr_samples script ↵AndreaGuarracino
in the blog as an example of how to parse metadata
2020-09-28new countries; updated genbank/sra scripts to manage more specimen sourcesAndreaGuarracino
2020-09-28genbank and sra scripts more picky on the ontologies; added utils.py for ↵AndreaGuarracino
shared functions
2020-09-27Virtuoso uploader: instructionsPjotr Prins
2020-09-27Virtuoso uploader: explicit outputPjotr Prins
2020-09-27Fixing missing dot in .ttl filelltommy
2020-09-27Adding script supporting semantic enrichmentlltommy
2020-09-26script for processing the metadata of the ESR samples; moved ↵AndreaGuarracino
delete_entries_on_arvados script in scripts directory
2020-09-25added new New Zealand entriesAndreaGuarracino
2020-09-04fixed bugs in in index management and type conversionAndreaGuarracino
2020-09-04sra script re-enabled, ready for testsAndreaGuarracino
2020-09-04added in the sra script an option to include only a subset of idsAndreaGuarracino
2020-09-04sra script updated for managing more locationsAndreaGuarracino
2020-09-04synchronized the create_sra_metadata.py script with the latest updatesAndreaGuarracino
2020-08-29fixed few countries ontology terms; added a new speciesAndreaGuarracino
2020-08-28added control (locally and in the validation) that sample_id has to be the ↵AndreaGuarracino
same in the metadata and in the FASTA header #103
2020-08-27updated dependency from clustalw to minimap2; the genbank script no longer ↵AndreaGuarracino
creates YAML/FASTA pairs for too short sequences
2020-08-26added option in the genbank script to ignore (already validated) IDs; code ↵AndreaGuarracino
cleaning; typos
2020-08-25the YAML/FASTA pair is not created for samples where at least one mandatory ↵AndreaGuarracino
field is missing
2020-08-24fixed protocol for the dictionary entries that caused validation problemsAndreaGuarracino
2020-08-23genbank/sra scripts update to be more generic with the specimen sourcesAndreaGuarracino
2020-08-23added new countries and speciesman sources: fixed few country entriesAndreaGuarracino
2020-08-22genbank/sra scripts updated to read the dictionaries in a more general wayAndreaGuarracino
2020-08-22lots of new dictionary termsAndreaGuarracino
2020-07-17Comment out some broken links for nowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-17Preparing for EBI submissionPjotr Prins
2020-07-17Started EBI submissionPjotr Prins
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