Container does not to work

[mictadlo]

Hi,
I can't access Sequence-server ( http://localhost:4567 ) in the browser after I did the following steps:

$ wget -c https://github.com/wurmlab/sequenceserver/archive/refs/tags/2.0.0.tar.gz
$ vim docker-compose.yml
$ cat docker-compose.yml 
sequenceserver:
  build: sequenceserver-2.0.0
  restart: always
  ports:
    - "4567:4567"
  volumes:
    - ./data/sequenceserver:/db

$ docker-compose build
...
Installing slop 3.6.0
Using sequenceserver 2.0.0 (was 2.0.0.rc8) from source at `.`
`/sequenceserver/bin/sequenceserver` does not exist, maybe `gem pristine sequenceserver` will fix it?
Bundle complete! 8 Gemfile dependencies, 11 gems now installed.
Gems in the group development were not installed.
Use `bundle info [gemname]` to see where a bundled gem is installed.
...
Get:16 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB]
Get:17 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2278 kB in 0s (12.2 MB/s)
Selecting previously unselected package libkeyutils1:amd64.
(Reading database ... 8611 files and directories currently installed.)
...
Step 38/45 : RUN npm install
 ---> Running in dd5eeabde4c3
npm WARN deprecated @stylelint/postcss-markdown@0.36.2: Use the original unforked package instead: postcss-markdown
npm WARN deprecated source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
npm WARN deprecated urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
npm WARN deprecated resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
npm WARN deprecated source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
npm WARN deprecated har-validator@5.1.5: this library is no longer supported
npm WARN deprecated uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
npm WARN deprecated request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
npm WARN deprecated tar@2.2.2: This version of tar is no longer supported, and will not receive security updates. Please upgrade asap.
npm WARN deprecated core-js@1.2.7: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
npm WARN deprecated core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
npm WARN deprecated core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.

added 744 packages, and audited 745 packages in 49s
...
Run `npm audit` for details.
npm notice 
npm notice New major version of npm available! 7.7.6 -> 8.6.0
npm notice Changelog: <https://github.com/npm/cli/releases/tag/v8.6.0>
npm notice Run `npm install -g npm@8.6.0` to update!
npm notice 
Removing intermediate container dd5eeabde4c3
...

$ sudo docker-compose up
Creating portal_sequenceserver_1 ... done
Attaching to portal_sequenceserver_1
sequenceserver_1  | stty: 'standard input': Inappropriate ioctl for device
sequenceserver_1  | [2022-04-06 05:40:16] INFO  Reading configuration file: /root/.sequenceserver.conf.

What did I miss?

Thank you in advance,

Michal

[MatthAlex]

Hi Michal,

I've reproduced your issue. I'm assuming that the end of the build log is something like this:

Removing intermediate container 486fa322b937
 ---> d8f01b3fcdee

Step 42/45 : FROM final AS minify
 ---> f4fb6b7093b7
Step 43/45 : COPY --from=node /usr/src/app/public/sequenceserver-*.min.js public/
 ---> affceb43ecfc
Step 44/45 : COPY --from=node /usr/src/app/public/css/sequenceserver.min.css public/css/
 ---> 3c4c2f2eddcd

Step 45/45 : FROM final
 ---> f4fb6b7093b7

Successfully built f4fb6b7093b7
Successfully tagged seqserv-test_sequenceserver:latest

If so, there seems to be a bug in docker that produces the stty: 'standard input': Inappropriate ioctl for device error. One workaround seems to be adding tty = true in docker-compose.yml config file. Can you try that?

[mictadlo]

Thank you, tty: true removed the error, but now it stuck at:

$ docker-compose up
Recreating portal_sequenceserver_1 ... done
Attaching to portal_sequenceserver_1
sequenceserver_1  | [2022-04-21 00:53:38] INFO  Reading configuration file: /root/.sequenceserver.conf.
sequenceserver_1  | 
sequenceserver_1  | Could not find BLAST+ databases in: /db.
sequenceserver_1  | 
sequenceserver_1  | Search for FASTA files (.fa, .fasta, .fna) in '/db' and try
sequenceserver_1  | creating BLAST+ databases? [y/n] (Default: y).
sequenceserver_1  | 

and http://localhost:4567/ still does not work.

What did I miss?

[yannickwurm]

@MatthAlex @mictadlo - any progress on this one?

[ErwinP]

You need to be able to start the container in an interactive fashion.
It is stated here that you apparently need to add stdin_open: true , perhaps in conjunction with tty: true.

[yannickwurm]

Thank you @ErwinP