EBISPOT/gwas-utils

Issues

• Create a queuing mechanism for the pre-GWAS-SSF harmonisation

  #151 opened a year ago by jdhayhurst
  3

• Remove unpublished condition from harmonisation queueing strategy

  #134 opened 2 years ago by jdhayhurst
  0

• catch 255 errors with the solr indexing nf pipeline

  #127 opened 2 years ago by jdhayhurst
  0

• harmonisation queuing bug doesn't create parent directory

  #125 opened 2 years ago by jdhayhurst
  1

• set wall time to 24 hours for the solr indexing job

  #120 opened 2 years ago by jdhayhurst
  0

• Use a workflow manager for managing the solr indexing jobs on the cluster

  #115 opened 2 years ago by jdhayhurst
  4

• catalog plots need to run without dependencies on Noah cluster

  #111 opened 3 years ago by jdhayhurst
  1

• Add sumstats ftp log parser

  #114 opened 3 years ago by jdhayhurst
  1

• create entry point for epmc xml tools

  #108 opened 3 years ago by jdhayhurst
  7

• inconsistencies for betaUnit (api)/beta (web)

  #109 opened 3 years ago by mpage21
  1

• stop the depo to harmonisation sync from exiting when encountering problems

  #107 opened 3 years ago by jdhayhurst
  1

• move ftp sync from gitlab/singularity to cron/conda

  #102 opened 3 years ago by jdhayhurst
  3

• change implementation from singularity to conda for pipeline that moves sumstats from submission app

  #106 opened 3 years ago by jdhayhurst
  1

• harmonised files are removed and not replaced on FTP when a curator "unpublishes" then "publishes"

  #98 opened 3 years ago by jdhayhurst
  2

• file moving error for depo submissions

  #94 opened 3 years ago by jdhayhurst
  0

• Publication 32917775 keeps being reported in the daily sumstats release report

  #45 opened 3 years ago by jdhayhurst
  0

• bug in the binning of files in on the sumstats ftp

  #90 opened 3 years ago by jdhayhurst
  1

• dockerise the gwas-utils environment

  #78 opened 3 years ago by jdhayhurst
  1

• setup Gitlab CI/CD for deploying gwas-utils to codon

  #72 opened 3 years ago by jdhayhurst
  1

• unpublish_study_export.py needs updating with new ftp structure

  #61 opened 4 years ago by jdhayhurst
  0

• provide text file listing harmonised data on ftp

  #62 opened 4 years ago by jdhayhurst
  0

• modify ftp sync for new structure and decouple from DB

  #51 opened 4 years ago by jdhayhurst
  0

• script to create structure on sumstats dirs

  #50 opened 4 years ago by jdhayhurst
  0

• modify script that feeds sumstats to staging

  #52 opened 4 years ago by jdhayhurst
  0

• modify harmonisation queuing and publishing step to account for new structure

  #53 opened 4 years ago by jdhayhurst
  0

• Update FTP Summary stats script to account for BoW submissions

  #20 opened 4 years ago by twhetzel
  12

• Review logging from script to get all unpublished studies

  #27 opened 4 years ago by twhetzel
  1

• sumstats formatting pipeline identifies file type

  #47 opened 4 years ago by jdhayhurst
  0

• pipe connecting the deposited sumstats to the harmonisation pipeline

  #34 opened 4 years ago by jdhayhurst
  1

• solr indexer stops prematurely

  #46 opened 4 years ago by jdhayhurst
  1

• Curation App 'Reports' tab error

  #42 opened 4 years ago by earlEBI
  2

• Update script to detect obsolete EFO terms

  #15 opened 5 years ago by twhetzel
  0

• permissions are not set correctly on folders in ftp

  #23 opened 4 years ago by jdhayhurst
  0

• For ftp sync, if study is in both unpublished and published tables it should proceed as though it is published

  #30 opened 4 years ago by jdhayhurst
  0

• As a user I want the GCP ID to be the unique and persistent identifier for my submitted dataset

  #29 opened 4 years ago by JalMacArthur
  2

• SumStats data release email report for unpublished studies

  #19 opened 4 years ago by earlEBI
  2

• Set-up the Curation queue script to run as a Bamboo job

  #16 opened 4 years ago by twhetzel
  2

• Improvements for the indexer manager

  #11 opened 5 years ago by DSuveges
  1