nathandunn
commented
6 years ago Well, there is a bit of work to be done unfortunately.
If you don’t need any advanced features of Apollo you could use the apollo-only branch, which is probably more of what you were looking for.
Conversely, you could use that and update this: https://github.com/GMOD/docker-apollo/blob/apollo-only/Dockerfile#L22 https://github.com/GMOD/docker-apollo/blob/apollo-only/Dockerfile#L22
To 6189ff9e2973e1523ddcdbeee9d258c435c42a54
A few questions that would help me help you:
1 - why do you need to use docker compose? 2 - ultimately what are you trying to accomplish?
You might want to take a look at this: https://github.com/galaxy-genome-annotation/docker-galaxy-genome-annotation https://github.com/galaxy-genome-annotation/docker-galaxy-genome-annotation. (They integrate multiple things within galaxy, including Apollo).
Natban
On Jul 3, 2018, at 6:06 PM, Michał T. Lorenc notifications@github.com wrote:
Hi, I set up docker-apollo inside a docker-compose.yml file:
apollo: image: quay.io/gmod/docker-apollo:latest restart: always ports:
- "8888:8080" volumes:
- ./data//jbrowse:/data
- ./data/postgres-data:/var/lib/postgresql While starting up I got the following Errors and Exceptions:
...
apollo_1 | WARNING: enabling "trust" authentication for local connections apollo_1 | You can change this by editing pg_hba.conf or using the option -A, or apollo_1 | --auth-local and --auth-host, the next time you run initdb. apollo_1 | Starting PostgreSQL 9.6 database server: main. apollo_1 | WEBAPOLLO_HOST_FLAG: apollo_1 | CHADO_HOST_FLAG: apollo_1 | Waiting for DB apollo_1 | /var/run/postgresql:5432 - accepting connections apollo_1 | Postgres is up, configuring database apollo_1 | psql: FATAL: Peer authentication failed for user "apollo-lqt" apollo_1 | Apollo database not found, creating... apollo_1 | CREATE ROLE apollo_1 | GRANT apollo_1 | Configuring Chado apollo_1 | psql: FATAL: Peer authentication failed for user "apollo" apollo_1 | Chado database not found, creating... apollo_1 | ERROR: role "apollo" already exists apollo_1 | GRANT apollo_1 | Loading Chado
...
apollo_1 | CREATE EXTENSION apollo_1 | psql:/chado.sql:49: ERROR: must be owner of extension plpgsql apollo_1 | SET
...
apollo_1 | ALTER TABLE apollo_1 | SET apollo_1 | psql:/chado.sql:2637928: ERROR: function create_point(integer, bigint) does not exist apollo_1 | LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000)) apollo_1 | ^ apollo_1 | HINT: No function matches the given name and argument types. You might need to add explicit type casts. apollo_1 | QUERY: SELECT box (create_point(0, $1), create_point($2,500000000)) apollo_1 | CONTEXT: SQL function "boxrange" during inlining apollo_1 | CREATE INDEX
...
apollo_1 | Loaded Chado apollo_1 | Restarting tomcat with /usr/local/tomcat/ apollo_1 | Jul 04, 2018 10:25:47 AM org.apache.catalina.startup.Catalina stopServer apollo_1 | SEVERE: Could not contact [localhost:[8005]]. Tomcat may not be running. apollo_1 | Jul 04, 2018 10:25:47 AM org.apache.catalina.startup.Catalina stopServer apollo_1 | SEVERE: Catalina.stop: apollo_1 | java.net.ConnectException: Connection refused (Connection refused) apollo_1 | at java.net.PlainSocketImpl.socketConnect(Native Method) apollo_1 | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) apollo_1 | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206) apollo_1 | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188) apollo_1 | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) apollo_1 | at java.net.Socket.connect(Socket.java:589) apollo_1 | at java.net.Socket.connect(Socket.java:538) apollo_1 | at java.net.Socket.
(Socket.java:434) apollo_1 | at java.net.Socket. (Socket.java:211) apollo_1 | at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:497) apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) apollo_1 | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) apollo_1 | at java.lang.reflect.Method.invoke(Method.java:498) apollo_1 | at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:406) apollo_1 | at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495) apollo_1 | apollo_1 | Tomcat started. ...
apollo_1 | Shiro Configured apollo_1 | 2018-07-04 10:26:36,175 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table allele add constraint FK_ssx0gv6xbtu3tbwt6ekkmn4iw foreign key (variant_id) references feature apollo_1 | 2018-07-04 10:26:36,179 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: constraint "fk_ssx0gv6xbtu3tbwt6ekkmn4iw" for relation "allele" already exists apollo_1 | 2018-07-04 10:26:43,169 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null apollo_1 | 2018-07-04 10:26:43,169 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" contains null values apollo_1 | 2018-07-04 10:26:49,561 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm apollo_1 | 2018-07-04 10:26:49,561 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist apollo_1 | Starting Quartz Scheduler in QuartzFactoryBean apollo_1
...
apollo_1 | 2018-07-04 10:27:47,437 [http-nio-8080-exec-6] WARN apollo.PreferenceService - No user present, so using the client token apollo_1 | 2018-07-04 10:27:47,486 [http-nio-8080-exec-3] ERROR apollo.PermissionService - Username not supplied so can not authenticate. apollo_1 | 2018-07-04 10:27:47,495 [http-nio-8080-exec-3] ERROR apollo.PermissionService - User null does not exist in the database. apollo_1 | 2018-07-04 10:27:47,549 [http-nio-8080-exec-10] ERROR authenticator.UsernamePasswordAuthenticatorService - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null. apollo_1 | 2018-07-04 10:27:47,550 [http-nio-8080-exec-10] WARN apollo.PermissionService - Failed to authenticate user apollo_1 | 2018-07-04 10:27:47,550 [http-nio-8080-exec-10] ERROR apollo.UserController - Failed to authenticate What did I miss?
Thank you in advance.
Michal
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mictadlo
Hi, I set up docker-apollo inside a
docker-compose.ymlfile:While starting up I got the following Errors and Exceptions:
What did I miss?
Thank you in advance.
Michal