jar: command not found

[John Reber]

I'm trying a fresh install of cBioPortal using docker compose.

I did the following:

git clone https://github.com/cBioPortal/cbioportal-docker-compose.git cd cbioportal-docker-compose

edited my .env file.

Ran ./init.sh

ran docker compose up -d

The cbioportal-container keeps restarting:

635f610cc02d   cbioportal/cbioportal:7.0.2          "/cbioportal/entrypo…"   About an hour ago   Restarting (127) 26 seconds ago                                                                                                    cbioportal-container
a6e8c8b81ac5   cbioportal/session-service:0.6.4     "/__cacert_entrypoin…"   About an hour ago   Up About an hour                                                                                                                   cbioportal-session-container
96fcc62e82e1   clickhouse/clickhouse-server:24.10   "/entrypoint.sh"         About an hour ago   Up About an hour (healthy)        0.0.0.0:8123->8123/tcp, :::8123->8123/tcp, 0.0.0.0:9000->9000/tcp, :::9000->9000/tcp, 9009/tcp   cbioportal-database-container
8e69166bab70   mongo:4.2                            "docker-entrypoint.s…"   About an hour ago   Up About an hour                  27017/tcp                                                                                        cbioportal-session-database-container

When I:

[cbioportal-docker-compose]$ docker logs cbioportal-container
/cbioportal/entrypoint.sh: line 5: jar: command not found
/cbioportal/entrypoint.sh: line 5: jar: command not found
/cbioportal/entrypoint.sh: line 5: jar: command not found
/cbioportal/entrypoint.sh: line 5: jar: command not found

the jar: command not found keeps repeating.

John Reber

[de Bruijn, Ino]

Hi John,

Apologies for the delay on this. We changed the docker image which excluded the jar so we did some workaround:

https://github.com/cBioPortal/cbioportal-docker-compose/pull/92

Hope that helps!

Best wishes,

Ino

From: 'John Reber' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Date: Wednesday, July 29, 2026 at 10:36 AM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] jar: command not found

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[John Reber]

Thanks for the update.

I was doing an apt-get install jdk in the entrypoint.sh, but that was playing havoc with java and AI just gave me this same fix today.  Wonder if it was gleamed from you?

Thanks,

John

------

John Reber
Systems Development Manager

Philadelphia, PA 19107
John....@jefferson.edu
KimmelCancerCenter.org

From: 'de Bruijn, Ino' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Date: Friday, August 14, 2026 at 4:12 PM
To: John Reber <John....@jefferson.edu>; cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>; Zhao, Gaofei <zh...@mskcc.org>
Subject: Re: [cbioportal] jar: command not found

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