coadunate/MICAS

Issues

• Run_fastq_watcher needs to run in background.

  #60 opened 2 years ago by syncrotron
  2

• Legacy code from Centrifuge

  #62 opened 2 years ago by syncrotron
  1

• final.out.paf file not being created with simulation

  #64 opened 2 years ago by tayabsoomro
  1

• Set up testing suite for email communications (test hooks and unit testing).

  #66 opened 2 years ago by syncrotron
  2

• comprehensive testing of FASTQ file listener on the browser and investigate ways to fortify it

  #68 opened 2 years ago by tayabsoomro
  1

• use mamaba to create conda environments

  #67 opened 2 years ago by tayabsoomro
  0

• Set up the auto-creation and location of the "MICAS location" within the setup page (somewhere like `~/.micas`). This also involves the removal of the option to input a path to the "MICAS location".

  #65 opened 2 years ago by syncrotron
  2

• Unhandled Rejection (Error): Network Error

  #61 opened 2 years ago by syncrotron
  1

• Install script need to be a little more sophisticated

  #31 opened 2 years ago by tayabsoomro
  3

• Simulating MinION Data injection

  #40 opened 2 years ago by tayabsoomro
  1

• Remove magic indexing from server/app/main/utils/FASTQFileHandler.py

  #59 opened 3 years ago by syncrotron
  0

• Add a check to see if the URL parameters are present before getting them

  #45 opened 3 years ago by tayabsoomro
  0

• Experiment centrifuge run with combined and individual indexes

  #10 opened 3 years ago by tayabsoomro
  1

• Remedy space issue in database downloading.

  #5 opened 3 years ago by tayabsoomro
  1

• Centrifuge fails to compile on WLS

  #47 opened 3 years ago by syncrotron
  1

• Be able to re-start the polilng system on any project

  #52 opened 3 years ago by tayabsoomro
  1

• Remove dependency on Tayabs email for Entrez.email

  #50 opened 3 years ago by syncrotron
  1

• npm install "Cannot find module [X]"

  #55 opened 3 years ago by syncrotron
  0

• SocketIO blocked by CORS

  #54 opened 3 years ago by tayabsoomro
  2

• Celery throws EOF error when downloading database

  #44 opened 3 years ago by tayabsoomro
  0

• An all-encompasing script that starts up the entire MICAS suite of programs

  #33 opened 3 years ago by tayabsoomro
  3

• After the "Create Database" button is clicked, we need indication that the database is being downloaded

  #29 opened 3 years ago by tayabsoomro
  2

• Stream the celery output into the webpage

  #28 opened 3 years ago by tayabsoomro
  1

• Central Logging System

  #53 opened 3 years ago by tayabsoomro
  0

• Documentation on how to start everything up

  #27 opened 3 years ago by tayabsoomro
  1

• Connect the front-end UI to the backend

  #35 opened 3 years ago by tayabsoomro
  0

• use YAML configuration file for programmatic method of building the analysis

  #49 opened 3 years ago by tayabsoomro
  1

• ~/.micas file needs to be created automatically

  #51 opened 3 years ago by tayabsoomro
  0

• Are spaces acceptable in database and incoming read path?

  #48 opened 3 years ago by syncrotron
  0

• Try to run MICAS on mk1c

  #43 opened 3 years ago by tayabsoomro
  0

• Get the front-end UI ready

  #34 opened 3 years ago by tayabsoomro
  1

• Update depreciated requirments

  #37 opened 3 years ago by syncrotron
  1

• Convert project to exclusivly use conda

  #36 opened 3 years ago by syncrotron
  1

• Activating the env doesn't work in install script

  #26 opened 3 years ago by tayabsoomro
  2

• Check `npm` is installed

  #38 opened 3 years ago by syncrotron
  0

• R package is required for install script

  #30 opened 3 years ago by tayabsoomro
  4

• Warning that centrifuge-build is not installed should be more clear

  #39 opened 3 years ago by syncrotron
  2

• PyYAML cannot uninstall warning with PIP

  #32 opened 3 years ago by tayabsoomro
  6

• Refine install script

  #24 opened 3 years ago by tayabsoomro
  2

• Create a flowchart of the entire process of MICAS

  #25 opened 3 years ago by tayabsoomro
  0

• Change alert threshold visualization code from fusioncharts to D3js

  #15 opened 6 years ago by tayabsoomro
  0

• Make the timeline functional

  #9 opened 6 years ago by tayabsoomro
  1

• Retrieving data from sankey.data

  #13 opened 6 years ago by tayabsoomro
  0

• Sankey visualization is not legible for porecamp data

  #8 opened 6 years ago by tayabsoomro
  3

• krakenParse function incorrectly generates the Sankey Plot.

  #14 opened 6 years ago by tayabsoomro
  1

• Set up email configuration

  #12 opened 6 years ago by tayabsoomro
  1

• Set up config file for Twilio

  #11 opened 6 years ago by tayabsoomro
  0

• SankeyPlot should also show unclassified reads

  #7 opened 6 years ago by tayabsoomro
  0

• Send task for sequence classification to the background

  #6 opened 6 years ago by tayabsoomro
  0

• Database index is not being built.

  #4 opened 6 years ago by tayabsoomro
  0