How to delete a locked bank?

Under certain conditions BioMAJ locks a bank during processing (to avoid errors in downloaded files), if you get this error :

An error occured:
Bank is locked due to an other action

To delete the bank, simply start by deleting the.lock file corresponding to the bank:

rm lock/alu.lock

Then remove the bank (for example in microservice):

biomaj-cli.py --proxy http://biomaj-publix-proxy:5000 --api-key XYZ --remove --bank alu

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How to solve an installation error with requests and influxdb?

pip install --upgrade pip
easy_install pip
pip uninstall requests 
pip install requests

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Where to find more examples of bank. properties file?

Here.

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Where to find more examples of process scripts?

Here.

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How to manage the administrator part of BioMAJ?

Here.

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Where is the documentation of the BioMAJ API?

Here.

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How to run FTP server in docker?

  • Change FTP ports in the docker-compose file (biomaj-docker/docker-compose.yml)
 biomaj-ftp:
     image: osallou/biomaj-docker
     volumes:
         - ${BIOMAJ_DIR}/biomaj:/var/lib/biomaj/data
     environment:
         - BIOMAJ_USER_PASSWORD=${BIOMAJ_USER_PASSWORD}
          - BIOMAJ_CONFIG=/etc/biomaj/config.yml
          - REDIS_PREFIX=biomajftp
          - RABBITMQ_USER=biomaj
          - RABBITMQ_PASSWORD=biomaj
     depends_on:
          - biomaj-mongo
          - biomaj-consul
          - biomaj-user-web
          - biomaj-elasticsearch
     ports:
          - "2121:21"
          - "6000-6010:6000-6010"
     command: bash -c "sleep 10 ; python3 /root/biomaj-ftp/bin/biomaj_ftp_service.py"
  • Change FTP ports in the config file (biomaj-docker/biomaj-config/config.yml):
ftp: listen: '0.0.0.0' 
port: 21  
passive_ports_start: 6000 
passive_ports_end: 6010

Increase timeout to initialize port:

export DOCKER_CLIENT_TIMEOUT=6000000000000000
export COMPOSE_HTTP_TIMEOUT=60000000000000000

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Which metrics are used in BioMAJ?

Here.

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How to migrate BioMAJ? (from BioMAJ 1 or BioMAJ 3X)

Here.

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How do the sessions work in BioMAJ?

Here.

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How to write process?

Here.

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How to modify and use your own global.properties with docker ?

Here.

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How to use the BioMAJ watcher?

BioMAJ Watcher (BW) has been designed to provide a quick overview of the banks managed by BioMAJ and a simple access to the most common administration tasks (display available banks and versions with main information(location, etc.). It is an optional web interface.

(GenOuest Example)

Here.

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How to cite BioMAJ?

Here.

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Who uses BioMAJ?

Here.

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How does the BioMAJ Workflow work?

Here.

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What is the license of BioMAJ?

Here.

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How to solve a download problem?

BioMAJ is blocked on the download part:

2018-03-06 04:24:18,984 DEBUG [root][MainThread] Rate limiting: 3
2018-03-06 04:24:18,984 DEBUG [root][MainThread] Workflow:wf_download:RemoteDownload:submitted: 3, current progress: -1, total: 22
2018-03-06 04:24:18,984 DEBUG [root][MainThread] Workflow:wf_download:RemoteDownload:RequestAvailable:-1
2018-03-06 04:24:29,020 DEBUG [root][MainThread] Rate limiting: 3
2018-03-06 04:24:29,020 DEBUG [root][MainThread] Workflow:wf_download:RemoteDownload:submitted: 3, current progress: -1, total: 22
2018-03-06 04:24:29,020 DEBUG [root][MainThread] Workflow:wf_download:RemoteDownload:RequestAvailable:-1
2018-03-06 04:24:39,052 DEBUG [root][MainThread] Rate limiting: 3

Try to reduce the files. num. threads option in the <bank>.properties file:

 #######################
### Synchronization ###
#######################

files.num.threads=2
protocol=ftp

 

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How to create influxdb database in biomaj-docker?

You will first have to run the CLI influxdb in the influxdb container and then create a biomaj database:

docker exec -it biomajdocker_biomaj-influxdb_1 influx
#Connected to http://localhost:8086 version 1.3.0
#InfluxDB shell version: 1.3.0
create database biomaj

More information Here.

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How to speed up downloads?

Increase the number of biomaj-download-web and biomaj-download message containers (1 web for 1 message). Indeed, the number of threads (files.num.thread) should not be too large because the number of connection is often limited by the remote server.

docker-compose scale biomaj-download-message=4
docker-compose scale biomaj-download-web=4

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How to simplify tools installation with Conda and BioMAJ?

Here.

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