Version 1 (modified by robert@…, 3 years ago)

Initial setup of configuration documentation

Configuration

You can configure the sequencing module by editing the file

  ~/grails-config/[environment]-massSequencing.properties

where [environment] will be the environment the war has been created for. Normally this will be 'prod'. If you have created your own package, the environment name might be different.

File contents

The file might look like the following

# server URL
grails.serverURL=http://massSequencing.dbnp.org

# DATABASE
dataSource.driverClassName=org.postgresql.Driver
dataSource.dialect=org.hibernate.dialect.PostgreSQLDialect
dataSource.url=jdbc:postgresql://localhost:5432/metagenomics-test
dataSource.dbCreate=update
dataSource.username=metagenomics
dataSource.password=dbnp
#dataSource.logSql=true

# GSCF configuration - in order to synchronize correctly
gscf.baseURL=http://studies.dbnp.org
massSequencing.consumerID=http://metagenomics.dbnp.org
massSequencing.synchronization = true

# File uploads
massSequencing.fileUploadDir=/tmp/metagenomics/temp
massSequencing.fileDir=/tmp/metagenomics/permanent

# Filename of the (.fna, .qual and .oligos) files that are exported
massSequencing.exportFilename=1.TCA.454Reads

Parameters

The different options you can set are:

grails.serverURL::

The url where this module is placed on. Don't add a trailing /

database.*::

Datasource configuration. See  http://grails.org/doc/latest/guide/3.%20Configuration.html#3.3%20The%20DataSource

gscf.baseURL:

Base URL of GSCF instance. Don't add a trailing /

massSequencing.consumerID::

Consumer ID describing this module. This is used for synchronization with GSCF. Set to the same value as grails.serverURL, unless you know what you're doing.

massSequencing.synchronization::

If set to true, the module will synchronize its studies with GSCF. If set to false, this module won't communicate with GSCF for synchronization (only for authorization). However, if set to false, you won't be able to add any data to the system. So use it only if you know what you're doing.

massSequencing.fileUploadDir::

Directory where uploaded files will be permanently stored. This is used for sequence files, quality files etc. that have been associated with a sample. If the directory is given relative (e.g. 'fileuploads/temp'), it is taken relative to the web-app directory. Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences'). The directory should be writable by the webserver user

massSequencing.fileDir::

Directory where uploaded files will be temporarily stored. This directory is used to store files when they are just uploaded. Files in this directory will be deleted when they are older than massSequencing.fileUploadMaxAge. If the directory is given relative (e.g. 'fileuploads/temp'), it is taken relative to the web-app directory. Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences'). The directory should be writable by the webserver user

massSequencing.fileUploadMaxAge::

Maximum age that uploaded files should be kept on the server before deleting them. When a user uploads a file, but doesn't process the file (e.g. because he leaves the page beforehand or his computer crashes), the files remain in the upload directory. This mechanism ensures that the upload directory is cleaned after some time. The time is given in seconds.