api port issue during installation

[MouCH]

Hi,
I am trying to install g2p aggregator on Mac but I am not used to docker and elastic search.
I get the following issue when I try to launch the docker compose :

ERROR: The Compose file './docker-compose-aws.yml' is invalid because:
services.api.ports is invalid: Invalid port ":", should be [[remote_ip:]remote_port[-remote_port]:]port[/protocol]

How can I resolve that ?

Thanks,

Charlotte

[Alex H. Wagner, PhD]

Hi @cmouden. Are you using the instructions for starting up the docker container? It looks like this error might be caused by omitting the ELASTIC_PORT and KIBANA_PORT env variables. You may optionally set these globally in your environment.

[MouCH]

Hi, Thank you for your answer. Actually these two variables are set, but it seems that the issue comes from the port for connecting the api to elastic : (base) cmouden:g2p-aggregator cmouden$ docker-compose -f docker-compose-aws.yml up -d WARNING: The API_PORT variable is not set. Defaulting to a blank string. WARNING: The ES variable is not set. Defaulting to a blank string. WARNING: The SWAGGER_HOST variable is not set. Defaulting to a blank string. WARNING: The SERVER_NAME variable is not set. Defaulting to a blank string. WARNING: The ADMIN_EMAIL variable is not set. Defaulting to a blank string. ERROR: The Compose file './docker-compose-aws.yml' is invalid because: services.api.ports is invalid: Invalid port ":", should be [[remote_ip:]remote_port[-remote_port]:]port[/protocol] Moreover, I've tried to use the jupyter version but I got this issue :/ : W: Failed to fetch http://httpredir.debian.org/debian/dists/jessie-updates/InRelease Unable to find expected entry 'main/binary-amd64/Packages' in Release file (Wrong sources.list entry or malformed file) It would really be great if I'll be able to run this tool... It looks useful! Best regards, Charlotte

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________________________________ De : Alex H. Wagner, PhD <[e-mail]> Envoyé : mercredi 8 mai 2019 00:33 À : ohsu-comp-bio/g2p-aggregator Cc : MouCH; Mention Objet : Re: [ohsu-comp-bio/g2p-aggregator] api port issue during installation (#134) Hi @cmouden<https://github.com/cmouden>. Are you using the instructions<https://github.com/ohsu-comp-bio/g2p-aggregator/blob/v0.12/README.md#docker> for starting up the docker container? It looks like this error might be caused by omitting the ELASTIC_PORT and KIBANA_PORT env variables. You may optionally set these globally in your environment. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#134 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AKXEFVXZHGDRFR5RUAJUD7DPUH7TLANCNFSM4HLJUS5A>.

[Alex H. Wagner, PhD]

Hi Charlotte,

You mentioned that you're running this locally, on your mac? Assuming you've got docker installed and running on your local machine, you will want to use the standard docker-compose (not the aws / Amazon Web Services one):

ELASTIC_PORT=9200 KIBANA_PORT=5601 docker-compose up -d

Do you still get the same error when running the above command?