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2020-05-06Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-05-05Add back necessary form-swapping javascript•••This partially reverts 03cbed808805ccdbff639eaa67e8f8b26c7275b3. Unless we actually take the inactive form fields out of the form in the DOM, their "required" attributes will prevent form submission. We can't just hide them. Adam Novak
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 reuse•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-04bump jerven/spodgi image to 0.0.6•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-04Remove debug flag from workflow submit•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-04add pangenome browser prepMichael R. Crusoe
2020-05-04Increase RAM for minimap2•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-03Set a RAM requirement on odgi_to_rdf to influence it to run on c5•••(because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-01Set verison tag on spodgi container image•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-30Merge pull request #47 from AndreaGuarracino/patch-15•••fixed UO_0000036 for yearPeter Amstutz
2020-04-30fixed UO_0000036 for yearAndrea Guarracino
2020-04-30Add py-dateutil to dependencies.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-30Handle running in a container with no username•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-30Last addition/edits to the meta data schemalltommy
2020-04-30Merge pull request #41 from AndreaGuarracino/patch-14•••the date is now handled more formally (YYYY-MM-DD)LLTommy
2020-04-30Import script fixes•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-30Wrap import script to run as a workflow•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-29Fix description content type for PyPi•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-29Add reference•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-29the date is now handled more formally•••all the date are saved as "YYYY-MM-DD"Andrea Guarracino
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-13•••updated the script to manage list field, and added new terms into the dictsLLTommy
2020-04-28updated to manage list fields and added new control on nasopharyngeal/throat ...Andrea Guarracino
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 image•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-28Call clustalw to compare sequence to reference•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
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 makes...lltommy
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 BonfaceKilz/feature/display-results-of-api-consum...•••Feature/display results of api consumptionLLTommy
2020-04-26Merge from remote branch into feature/display-results-of-api-consumptionBonfaceKilz
2020-04-26Update styles to match suggested mockup•••Ref: https://xd.adobe.com/view/fa2b4841-e463-432e-7465-e96b4ed200ff-8c1a/screen/b84fcf66-9580-4ae2-b37d-7ee15401d627/Pangenome-Browser-Manual-Metadata-Host BonfaceKilz
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
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