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2020-11-04Fix typoBonfaceKilz
2020-11-04virtuoso-ose: install and settingsPjotr Prins
2020-11-04fixed sequence_assembly_method field descriptionAndreaGuarracino
2020-11-04Test data setPjotr Prins
2020-10-30Adding some more wikidata locationslltommy
2020-10-28Country informationPjotr Prins
2020-10-28List by country and added to mapPjotr Prins
2020-10-28Fix DEMO linksPjotr Prins
2020-10-28Adding more metadata to resource uriPjotr Prins
2020-10-28Create permalink and some outputPjotr Prins
2020-10-28Use Flask url_for to make relative routes workPjotr Prins
2020-10-28Fix CSS errorsPjotr Prins
2020-10-27Commented in uploader main.pyPjotr Prins
2020-10-27Updating docsPjotr Prins
2020-10-26Update blogPjotr Prins
2020-10-26Minor CSS for the mapPjotr Prins
2020-10-26Improved map to show sequences in one viewPjotr Prins
2020-10-26Adding upload metadata examplesPjotr Prins
2020-10-26Textual updatesPjotr Prins
2020-10-06Create .dockstore.ymlMichael R. Crusoe
2020-10-01sequence divergence to 5% for minimap2 in the FASTA quality controlAndreaGuarracino
2020-10-01show more information in the error messagesAndreaGuarracino
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
2020-09-27Adding a few labels to other used vocabslltommy
2020-09-27Updated country labels and GPS coordinateslltommy
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
2020-09-05increased the quality filter thresholdAndreaGuarracino
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 script to remove entries on ArvadosAndreaGuarracino
2020-08-28local QC is optionalAndreaGuarracino
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
2020-08-28qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵AndreaGuarracino
a time; code cleaning
2020-08-28fixed local QC, modifying the regex for FASTA/FASTQ to be more generalAndreaGuarracino
2020-08-27updated dependency from clustalw to minimap2; the genbank script no longer ↵AndreaGuarracino
creates YAML/FASTA pairs for too short sequences
2020-08-26Increase RAM for odgi-build-from-spoa-gfaPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-26updated parameter nameAndreaGuarracino
2020-08-26added option in the genbank script to ignore (already validated) IDs; code ↵AndreaGuarracino
cleaning; typos
2020-08-26typos in the code; little code refactoringAndreaGuarracino
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