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2020-05-05Use invisible class instead of hidden classAdam Novak
2020-05-05Add JS at front end for lists, and date support on backendAdam Novak
2020-05-05Handle doubles and lists on the backendAdam Novak
2020-05-05preserve the directory layout of segmentation.pyMichael R. Crusoe
2020-05-05move some tools into the shared repoMichael R. Crusoe
2020-05-04Sort input to hopefully get container reusePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04bump jerven/spodgi image to 0.0.6Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04Remove debug flag from workflow submitPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04add pangenome browser prepMichael R. Crusoe
2020-05-04Increase RAM for minimap2Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-03Set a RAM requirement on odgi_to_rdf to influence it to run on c5Peter Amstutz
(because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-01Set verison tag on spodgi container imagePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Merge pull request #47 from AndreaGuarracino/patch-15Peter Amstutz
fixed UO_0000036 for year
2020-04-30fixed UO_0000036 for yearAndrea Guarracino
2020-04-30Add py-dateutil to dependencies.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Handle running in a container with no usernamePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Last addition/edits to the meta data schemalltommy
2020-04-30Merge pull request #41 from AndreaGuarracino/patch-14LLTommy
the date is now handled more formally (YYYY-MM-DD)
2020-04-30Import script fixesPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Wrap import script to run as a workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Fix description content type for PyPiPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Add referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29the date is now handled more formallyAndrea Guarracino
all the date are saved as "YYYY-MM-DD"
2020-04-29fixing JS due to name changes so the demo works againlltommy
2020-04-29Reverting country list back, something went wrong therelltommy
2020-04-29Merge pull request #40 from AndreaGuarracino/patch-13LLTommy
updated the script to manage list field, and added new terms into the dicts
2020-04-28updated to manage list fields and added new control on nasopharyngeal/throat ↵Andrea Guarracino
swab
2020-04-28Updated with new termsAndrea Guarracino
2020-04-28Updated with new termsAndrea Guarracino
2020-04-28Updated - 1731 IDs - 2020/04/28Andrea Guarracino
2020-04-28Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-28Decision to settle for float instead of integers for the coveragelltommy
2020-04-28Update spodgi docker imagePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Call clustalw to compare sequence to referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Whatever happend to the minimal metadata, I restored itlltommy
2020-04-28Adding field 'publication' to the maximum examplelltommy
2020-04-28Changes to the structure - we use lists now instead of strings where it ↵lltommy
makes sense. This allows us to have multiple values where in makes sense
2020-04-26Add enrichment vocabularies to gitlltommy
2020-04-26Pushing some new functions, rename some old oneslltommy
2020-04-26Adding a function, correcting some variable nameslltommy
2020-04-26Updating dicslltommy
2020-04-26Merge pull request #39 from ↵LLTommy
BonfaceKilz/feature/display-results-of-api-consumption Feature/display results of api consumption
2020-04-26Merge from remote branch into feature/display-results-of-api-consumptionBonfaceKilz
2020-04-26Update styles to match suggested mockupBonfaceKilz
Ref: https://xd.adobe.com/view/fa2b4841-e463-432e-7465-e96b4ed200ff-8c1a/screen/b84fcf66-9580-4ae2-b37d-7ee15401d627/Pangenome-Browser-Manual-Metadata-Host
2020-04-26Display the output of the queries as prettified JSON for nowBonfaceKilz
2020-04-26Jsonify response and pick the valuesBonfaceKilz
2020-04-26Add basic structure for interacting with the APIBonfaceKilz
2020-04-26Remove unnecessary JSBonfaceKilz
2020-04-26Put JS code in its own JS fileBonfaceKilz
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