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, PLUGIN or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA, PLUGIN and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value. You can use multiple PREFIX instructions through-out the session, they will each be valid for the following DATA, PLUGIN and CONFIG instructions, until reset with an alternative value. |
| OPTION | Key=value definition of a single configuration option. This is suited to override a few config options as needed. |
| ALIAS [primary name]=[display 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. Multiple primary names can point to the display name, in that case you can use the aliases to connect multiple different IDs. |
| 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 ALIAS MT_H37RV_V2=MyTBGenome DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta PREFIX http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/ DATA annotation.gff DATA operon.gff DATA sRNA.gff DATA rRNA.gff PREFIX PLUGIN http://www.broadinstitute.org/software/genomeview/resources/save2pdf-1.1.zip
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>
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");