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Release 2.0 (merge dev to master)

Merged Release 2.0 (merge dev to master)
dev into master
Merged Loraine Gueguen requested to merge dev into master

General

  • Reorganize repository
  • Fix verbosity mode
  • Fix logs details
  • Update README.md
  • Update the "help" option in the scripts
  • Update examples
  • Factorize and optimize code
  • Create file constants.py containing the constant variables

Input organisms.yml file

  • Change root structure (a list instead of a dictionary, the name parameter is added to the species dictionary sp_dict)
  • Add parameter main_species. Useful when there are multiple strains for the same species: set to yes to define the strain used as home for JBrowse
  • Parameters species, genus, strain, sex, common will be sanitized (removing " ", "-", "(", ")", "'")
  • Add jinja2 template

Input config file

  • Change root structure (one-level dictionary)
  • Add parameters authelia_secrets_env_path and authelia_db_postgres_password required for Authelia
  • Change the name of some parameters (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url)
  • Remove unused apollo parameters (webapollo_user, webapollo_password)

Step "init"

  • Update templates files
  • Fix the copy of the specified banner
  • Write galaxy_nginx.conf only if needed

Step "get data"

  • Prefix data filenames with g_species_s
  • Add the last modification date of the source file to the gff filename

Step "load data"

  • Use Bioblend function upload_from_galaxy_fs() instead of upload_from_local() (to enable symlink, instead of copy)

Step "run workflow Phaeoexplorer"

  • Development of a workflow loading fasta and gff files to Chado, Tripal and JBrowse, for one or two organisms of the same species
Edited by Loraine Gueguen

Merge request reports

Merged by Loraine GueguenLoraine Gueguen 3 years ago (May 16, 2021 3:37pm UTC)

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