Genepattern server docker installation

[ppdragon]

I tried run genepattern server in docker. The genepattern server  can not be started. Below are my steps, 

1.

docker pull genepattern/genepattern-server:v3.9.11-rc.5-b252

2.

docker run -it genepattern/genepattern-server:v3.9.11-rc.5-b252 /bin/bash

3.

cd /opt/genepattern

 ./StartGenepatternserver

(there is no output in the terminal),

4. Open browser on host, go 127.0.0.1:8080/gp, the server can not be started

Attached please find webserver.log and genepatter.log.

________________________________________

I also tired to run

./startgp-host.sh

in /gpinstall, get error:

 

lookup docker on 192.168.1.1:53 no such host

This looks like a very common error of Docker. I tried lots of things to fix it including editing /etc/resolv.conf add nameserver 8.8.8.8

But the error is the same.

Did I did someting run for genepattern-server docker?

My OS is Ubuntu 20, I tried MAC, and had the same error.

Thanks.

[Ted Liefeld]

Hi

you are jumping the gun on us a bit as we are just starting to write up the doc and process for running a GenePattern server in docker.  I can send you the current doc for it via a private message in the forum.  Since its not yet complete or QA'd I would rather not publish the doc publicly yet.

That said, I will try to set out the issues here in case others want to try this before we release.  

So far we have only run the server on docker in OSX but this should also work for linux.  The things that might be missing in your first attempt are

1. Port mapping - you need to map 8080 out to the host 

2. Drive mapping - we keep the jobResults, tasklib,  user and resources folder external to the container (mounted drive or docker volume) so they persist through GenePattern updates

3. docker.sock mapping - GenePattern needs to call the docker host to run modules so the docker.sock also has to be mounted to the container

4. configuration - the jobs.docker.bind.source in the GenePattern config_custom.yaml file must specify the root folder for the jobResults, tasklib, resources and user folders so that the module containers can access their contents as well.

 

When this is released there will be a script to do all this setup for you.  In the meantime I will send along the current doc privately.

Hope this helps

Ted

[ppdragon]

Yes, please send me the document. I would like to try it.

What is the platform that you recommend for local genepattern server? Linux or OSX.

I tried both, but neither of them works for me. I will ask in another post.

[Ted Liefeld]

You should have gotten the document in another message just a few minutes after the last one.  You might want to check your spam folder/trash.  as for platform, development was done on OSX

Ted

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Ted Liefeld                                      UC San Diego

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