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cmbi / kmad-web

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Docker #26

Closed jonblack closed 7 years ago

jonblack commented 7 years ago

This is a partial implementation for using docker. There are still some errors with the software dependencies that need fixing.

@joannalange You can add commits to this pull request. It'd be a great help if you could take a look.

joannalange commented 7 years ago

@jonblack, looks like it's working now, can you check it?

joannalange commented 7 years ago

@jonblack, can I merge it so that @cbaakman can deploy it on the server using docker?

cbaakman commented 7 years ago

@joanna I can clone jon's branch, I'm testing it right now. Anything specific I should look for?

joannalange commented 7 years ago

@cbaakman, when I tested it on my machine it seemed already to be working fine, I just couldn't check if all the big databases realted stuff is fine because they're mounted on the server

cbaakman commented 7 years ago

I detected an error, occurring while running docker-compose build:

Step 34 : RUN /deps/spined/bin/run_spine-d . 1crn
 ---> Running in b4069b58e11b
This is your first time running SPINE-D, some fortran codes need to be compiled.
Compile with gfortran...ok.
If you see error messages, please check your fortran compiler.
Compiling's done.
prepare... ok.
running psiblast... error running psiblast.
ERROR: Service 'celery' failed to build: The command '/bin/sh -c /deps/spined/bin/run_spine-d . 1crn' returned a non-zero code: 2

Are there any blast databank mounts required?

In the docker file it reads:

# Remove lines that check if the databanks are present. These will be       
# mounted later when the container runs.

However, there are no volumes in the docker-compose file.

joannalange commented 7 years ago

It does require the blast databases, so that's why it crashes ( it runs psiblast and psiblast needs them)

Jon said they would be mounted on the server, @jonblack?

jonblack commented 7 years ago

@cbaakman Should this be merged now? How does this differ to https://github.com/cmbi/kmad-web/pull/27?

cbaakman commented 7 years ago

I saw that you also made a pull request indeed. I don't know why that isn't merged though.

This version is based on your pull request, but also has an extra docker file that takes care of scheduling databank updates. (we might not want this, that's up to you)

I've tested it by running some alignments through the web interface. The unit and integration tests don't all succeed though, but I don't think that's because of docker.

jonblack commented 7 years ago

Closed in favour of #27.