Server Error 500

[TobiasWinter97]

Hi, I've successfully installed HydDB-webserver on my HPC.
My installation steps are as following:

$ singularity shell instance://singularity instance start --writable-tmpfs --net --network=none --bind /public/home/sammyzhao97/databases/hyddb:/db new_hyddb.sif hyddb_web
$ singularity shell instance://hyddb_web
$ cd /
$ mkdir db
$ touch db.sqlite3
$ cd /code
$ python manage.py makemigrations
$ python manage.py migrate
$ python manage.py loaddata hydrogenaseclass hydrogenasesequence geneticorganisation
$ python manage.py train
$ python manage.py trainupstream data
$ python manage.py runserver 0.0.0.0:port

On my mac:

ssh -L port:node:port sammyzhao97@server

Then I successfully open the server on my mac. But when I submit the job, it shows server error 500. How to fix this problem?

I upload the faa file and click the submit jobs button:

It shows server error:

And another problem:
When I click the browser button, it tells me error(url/hyddb/browser):

And after I remove the redundant /hyddb, it works (url/browser/).

And cannot properly show the images:

[TobiasWinter97]

Please help me out. Thanks a lot!

[jlingford]

Regarding classifier server error:

Hi, the classifier tool requires a number of dependencies (celery, rabbit, redis) to allow Django app to communicate with the sqlite database. This is why using docker compose is necessary. Since you are trying to run this on a HPC, you will probably have to use the equivalent singularity compose commands and probably also convert the docker-compose.yml file to a singularity-compose.yml file. The commands and .yml file contents will probably be the same or similar, but since I have only tried running the HydDB website through Docker and not Singularity, I'm not sure exactly what changes might need to be made.

Regarding broken image links:

It looks like you haven't mounted the media volume. See the docker-compose.yml file for all the volumes that need to be mounted. E.g.

volumes:
      - .:/code
      - ./media:/media
      - ./tmp/db:/db
      - ./tmp/blastdb:/blastdb
      - ./tmp/static:/static

So something like adding --bind /public/home/sammyzhao97/databases/hyddb/media:/media to your singularity command should work. But again, this should be done with docker compose / singularity compose.

Regarding browser url issue:

I've noticed this is an issue between trying to run the Django code locally (i.e. not from inside a container) and from inside the container. Try running everything with the docker compose / singularity compose steps and see if it's still an issue.

Regarding running from a HPC

Is there a particular reason you want to run this from a HPC as opposed to on your own machine? We have only tested this code with a Docker & docker compose setup so far, not singularity, so there may be issues we're not familiar with there. The HydDB classifier tool is lightweight and fast enough to run on a regular laptop, so if you need to do hydrogenase classification on a massive scale, I would recommend using another method.