iimog/bcdatabaser_web repository overview

⁠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!

⁠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

• 1.1.1 <2019-11-05> Add online documentation
• 1.1.0 <2019-11-03> Add orcid authentication
• 1.0.0 <2019-07-15> Initial stable release