Session files

Session files allow you to organize a large number of data files and config options in a single file.

An example session file:

http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php

You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.

File structure

Header

Make sure the file starts with a line that contains the words 'GenomeView' and 'session'. These two words have to be on the first line!

We recommend:

##GenomeView session

This header is used to detect the file format by GenomeView.

Body

The remainder of the file contains lines that have various instructions to load data, configure GenomeView or load plugins. The table below has an overview of all options.

Instruction*	Value
CONFIG	URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.
DATA**	URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.
PREFIX	URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.
OPTION	Key=value definition of a single configuration option. This is suited to override a few config options as needed.
ALIAS [primary name]=[alternative name].	Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.
LOCATION	Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].
PLUGIN	Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter

** The legacy keywords C, U and F will continue to work.

Each of the lines should be organized like this:

instruction[tab, colon or space]value

For example, all of these are valid ways to specify a file

DATA	http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff
DATA:http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff

Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.

Example session file

##GenomeView session -- DO NOT DELETE THIS LINE
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/sRNA.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/rRNA.gff
ALIAS MyTBGenome=MT_H37RV_V2

Starting a session with a launch URL

The basic set-up to start GenomeView with a session file is

http://genomeview.org/start/launch.jnlp?--session <URL to the session file>

For example http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php

Hiding the session URL

Typically you don't even have to expose this URL and you can use a simple PHP script index.php that redirects to that location. For example:

header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php");