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2020-11-09Make it so "pangenome analysis" only runs collect-seqs.Peter Amstutz
Will ensure that metadata is kept up to date. GFA isn't being generated. Will introduce new workflow that uses from_sparql to analyze a subset. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Rename schema param to metadataSchemaPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Extract subset of the all-sequences fasta by running a sparql query.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-08Uploaded UTHSC sequencesPjotr Prins
2020-11-08UTHSC samplesPjotr Prins
2020-11-07Tests: added SPARQL testPjotr Prins
2020-11-07Tests: add runner and frame for SPARQLPjotr Prins
2020-11-07RDF: use URIsPjotr Prins
2020-11-07Test: simplify and add regression testPjotr Prins
2020-11-07Fixed the License error (https!!)Pjotr Prins
2020-11-07Running tests without networkPjotr Prins
2020-11-07Added failing unit test: No matching triples found for predicate cc:LicensePjotr Prins
2020-11-06Add locationPjotr Prins
2020-11-06Add country entries that miss coordinatesPjotr Prins
2020-11-06Country trouble shootingPjotr Prins
2020-11-06Uploader script improvementsPjotr 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
2020-11-06Working on uploadPjotr Prins
2020-11-05Add 10 samplesPjotr Prins
2020-11-05Added notePjotr Prins
2020-11-05Using 'DOCS' instead of 'BLOG'Pjotr Prins
2020-11-05Updated API docPjotr Prins
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
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