nhoffman/ya16sdb

Issues

• Option to visualize sequence distribution without the outliers in the web interface

  #72 opened 3 months ago by marykstewart
  1

• Apply for an Amazon Open Data Sponsorship s3 bucket

  #75 opened 3 months ago by crosenth
  0

• Create outline for publication

  #40 opened 3 months ago by crosenth
  1

• Methods outline

  #74 opened 3 months ago by crosenth
  1

• Manuscript outline

  #73 opened 3 months ago by nhoffman
  1

• Add --{negative}-taxid support to Blast database(s)

  #69 opened 4 months ago by dhoogest
  0

• Web interface https://ya16sdb.labmed.uw.edu/ not operative?

  #65 opened 6 months ago by marykstewart
  2

• Slurm compatibility

  #64 opened 8 months ago by crosenth
  0

• migrate to ECS

  #53 opened 2 years ago by nhoffman
  5

• requirements.txt should pin all dependencies

  #56 opened a year ago by nhoffman
  0

• update pipeline Docker file to use python 3.11 and bookworm base

  #55 opened a year ago by nhoffman
  0

• create s3 bucket for data, automate upload of feather file

  #26 opened 6 years ago by nhoffman
  2

• Type strain record present in latest NCBI_16S build not visible on https://ya16sdb.labmed.uw.edu/

  #54 opened a year ago by marykstewart
  0

• include build instructions for singularity images

  #33 opened 6 years ago by nhoffman
  1

• gateway timeouts

  #50 opened 2 years ago by nhoffman
  2

• genome identifier

  #36 opened 2 years ago by nhoffman
  3

• Create a Dash Datatable to visualize seq_info.feather file

  #52 opened 2 years ago by crosenth
  0

• Records dropped as duplicates but then 'added back' as types are absent from named_type_hits output

  #45 opened 3 years ago by dhoogest
  2

• Checking my understanding of the 'type_classification' column in the new interface

  #51 opened 2 years ago by marykstewart
  2

• Create a runnable Docker image

  #41 opened 2 years ago by crosenth
  1

• Best match 16S type strain record in ya16sdb web interface does not match data in NGS16S output

  #44 opened 2 years ago by marykstewart
  2

• Use the labmed classifier to illustrate species uncertainty in Dash app

  #49 opened 3 years ago by crosenth
  2

• Move dash folder into its own repo

  #35 opened 3 years ago by crosenth
  0

• Split dash app legend into separate color and shape legends

  #19 opened 3 years ago by crosenth
  0

• Some accession feature tables returning duplicate feature coordinates

  #30 opened 3 years ago by crosenth
  4

• Distinguish 16S-only records from those that were extracted from whole genomes

  #32 opened 6 years ago by marykstewart
  3

• Add ANI tax check data to Dash app

  #46 opened 3 years ago by crosenth
  1

• bin/match_hits.py look top hit within same species

  #47 opened 3 years ago by crosenth
  1

• Investigate updating the Dash app html table into a DataTable

  #48 opened 3 years ago by crosenth
  0

• dash app sequence records showing themselves as closet type strain (match_species)

  #39 opened 4 years ago by crosenth
  1

• Publication status of NCBI records is not current

  #38 opened 4 years ago by marykstewart
  0

• regex bug for long genome accessions

  #37 opened 5 years ago by dhoogest
  3

• roll back https://github.com/nhoffman/ya16sdb/pull/31

  #34 opened 6 years ago by dhoogest
  2

• review dependencies in venv vs singularity images

  #27 opened 6 years ago by nhoffman
  1

• add settings-example.conf

  #28 opened 6 years ago by nhoffman
  1

• generate list of species represented in filter plots

  #29 opened 6 years ago by nhoffman
  0

• use singularity image for ncbi tools

  #25 opened 6 years ago by nhoffman
  0

• Remove creation of dedicated stack and add deployment to existing dokku instance

  #24 opened 6 years ago by nhoffman
  0

• Setup dash app LetsEncrypt plugin on Dokku

  #20 opened 6 years ago by crosenth
  1

• allow url-encoding of all selectors

  #23 opened 6 years ago by nhoffman
  2

• move axes to top of plot along with other selectors

  #22 opened 6 years ago by nhoffman
  1

• Add E faecalis, E faecium and E avium to the test data set feather file

  #21 opened 6 years ago by crosenth
  1

• view outliers app

  #16 opened 6 years ago by nhoffman
  5

• Add select and deselect all markers (glyphs) option to dash app

  #18 opened 6 years ago by crosenth
  0

• Wrong source specified for trusted types blastdb

  #17 opened 6 years ago by dhoogest
  2

• consider post-filtered 'type' sequences for target of vsearch

  #14 opened 6 years ago by dhoogest
  7

• non-species in dedup/1200bp/named/filtered

  #13 opened 6 years ago by nhoffman
  3

• Handle RefSeqs derived from other RefSeqs

  #15 opened 6 years ago by crosenth
  1

• seq_info.csv should be consistent among all subdirectories

  #12 opened 6 years ago by nhoffman
  2

• Add is_type column before dedup step

  #11 opened 6 years ago by crosenth
  1