checklist to ISMB abstract subm release

This is checklist for @vibaille and @rplanel of what needs to be done to get as of ISMB abstract submission deadline. Work branch for that is: to-final-gitlab-orga.

On the readme/doc/test data side:

  • drop testdata as testdata.csv in testdata folder. Make it minimal, one pheno, at most two for safety, no covariates.
  • Readme: general intro
  • Readme: how to retrieve the dockers, deploy, create
  • Readme: getting started: description of interface, 1st encounter, what to start with
  • Readme: load pheno data
  • Readme: annotate pheno data w pheno categories and controlled vocab
  • Readme: plot pheno data and transform if any
  • Readme : QTL mapping, the difft steps: format data, calc genoprob, scan, perm, find peaks & effects, ref regions
  • Readme: more advanced command. Permissions, data deletion... All what is not worth telling as 101
  • Readme: FAQ.
  • for all figs in readme, hyperlink to corresponding figs to be hosted in docs/img folder

Overall/general side:

  • cleanup to only have relevant dirs and files in to-final-gitlab-orga. List of (very old) things to check: .gitlab/issue_templates, classes_draft.mdj, classes_draft.png, start-docker-compose.sh
  • ensure https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db is publicly available
  • once all is done, merge to-final-gitlab-orga to main so that all appears at https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db (which is path provided in abstract)
  • Readme: after merging to main, fix all hyperlinks in readme
  • License file!! (oups)

... any other thing to add ?

Edited by Remi PLANEL