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About

Web interface for the BCdatabaser pipeline. Public instance hosted at: https://bcdatabaser.molecular.eco Documentation: https://molbiodiv.github.io/bcdatabaser/

Logo

The current logo is designed by @mirzazulfan. Thanks a lot Mirza! Logo

Hosting your own instance

Feel free to host your own instance of the BCdatabaser web server. To do so use the docker-compose.yml included in this repository. Don't forget to deposit a file .zenodo_token with your zenodo token. Also a file .env is required for OAuth via ORCiD with content like this:

ORCID_ID='YOUR-ID'
ORCID_SECRET='YOUR-KEY'
OAUTH_STATE='SOME-SECRET-STRING'
SESSION_SECRET='SOME-SECRET-STRING'

We recommend adding the following two entries to your host crontab to clean old job data every day and update the local NCBI Taxonomy dump once a week (see issue #15). Adjust the path to your folder containing the docker_compose.yml and the desired time and frequency of execution to your needs.

# m h  dom mon dow   command
10     5     *     *     *     cd /home/bcd/bcdatabaser_prod/ && docker-compose exec web find /tmp -maxdepth 1 -type d -ctime +2 -name "tmp-*" -exec rm -rf {} +
30     3     *     *     2     cd /home/bcd/bcdatabaser_prod/ && docker-compose exec web bash -c "cd /NCBI-Taxonomy/ && perl make_taxid_indizes.pl && cd /Krona/KronaTools/ && ./updateTaxonomy.sh"

LICENSE

This software is licensed under MIT. Be aware that the libraries and external programs are licensed separately (possibly under different licenses).

Changes

  • 1.1.2 <2021-11-10> Add retry download mechanic (#16, #31, #36), thanks to @LasKru
  • 1.1.1 <2019-11-05> Add online documentation
  • 1.1.0 <2019-11-03> Add orcid authentication
  • 1.0.0 <2019-07-15> Initial stable release