Metagenomic webservice to automatically analyse sequences
Right now it is just a bunch of scripts, quick and dirty methods to make the job done.
- Kraken2
- Bracken
- Pavian
- FastQC
- PHP
- Apache2
Be careful every component has it's own dependencies!
/home/services/qc: Place of FastQC /home/services/metagenomics: Put the files from 'service' of this repository to here. Also install Kraken2, Bracken here. Database should be here too. /var/www/html: Copy the files from 'web' of this repository to here. /home/upload: Users upload files to here
I have put the following line into crontab:
00 0 * * * root bash /home/services/metagenomics/analyse.sh >>/home/services/metagenomics/log/stdout.txt 2>>/home/services/metagenomics/log/stderr.txt
Every midnight the analysis.sh from /home/services/metagenomics run. Copy the uploaded files to another place, run FastQC, Kraken2, Bracken and put results into /var/www/html/metagenomics. Next day the users can see the results. There is no user interaction, because I do not want to train people and I do not have time to make helpdesk. If there is no interaction, users cannot brake anything.
However there are some limitation. The script assume the user upload gzipped, paired-end files and the length is 2x 150.
There is a shiny server in port 3838 with Pavian. Right now users need to download the report files and upload here to visualize the results.
The service right now does not store sequences. Delete it after process to prevent disk overflow.