OSError: Unable to open SeqRepo directory /usr/local/share/seqrepo/latest when using seqrepo

[algarsi3]

I followed the instructions to install and configure vrs-python.

$ docker ps
CONTAINER ID   IMAGE                                    COMMAND                  CREATED          STATUS          PORTS     NAMES
ba533a28fd60   biocommons/uta:uta_20180821              "docker-entrypoint.s…"   18 minutes ago   Up 18 minutes             stack_uta_1
888be6a91e11   biocommons/seqrepo-rest-service:latest   "seqrepo-rest-service"   18 minutes ago   Up 18 minutes             stack_seqrepo-rest-service_1

However, when I try to execute jupyter examples I get the following error:

HTTPError: 500 Server Error: INTERNAL SERVER ERROR for url: http://localhost:5000/seqrepo/1/sequence/NC_000019.10?start=44908821&end=44908822

I saw that there are two examples to test the containers in the docker-compose.yml file, while this works as expected:

$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from transcript'
249909

This returns e the same error described above:

$ curl -f http://0.0.0.0:5000/seqrepo/1/sequence/NP_001274413.1
curl: (22) The requested URL returned error: 500 INTERNAL SERVER ERROR

I can access to the http://localhost:5000/seqrepo/1/ui/ URL, but even when I try /ping I get the 500 error. Any ideas on how could I solver this?

[reece]

Confirmed problem. I'll need some more time to investigate the cause.

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This issue was marked stale due to inactivity.

[korikuzma]

Reopening because our lab is still getting this error. I had to change the docker-compose.yaml (removing network_mode: host and adding ports) as shown below:

version: "3"

services:
  seqrepo-rest-service:
    ports:
      - 5000:5000
    # Test: curl http://localhost:5000/seqrepo/1/sequence/refseq:NM_000551.3
    image: biocommons/seqrepo-rest-service:latest
    volumes:
      - seqrepo_vol:/usr/local/share/seqrepo

  uta:
    ports:
      - 5432:5432
    # Test:
    # psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from transcript'
    # 249909
    image: biocommons/uta:uta_20180821
    volumes:
      - uta_vol:/var/lib/postgresql/data

volumes:
  seqrepo_vol:
    external: true
  uta_vol:
    external: true

@reece I know it's been a long time since you looked at this, but you be able to assist with this again?

[reece]

@korikuzma : Yes, looked briefly tonight and will need another day or two.

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This issue was marked stale due to inactivity.