This page has been replaced with this page (https://github.com/GMOD/jbrowse/wiki/JBrowse_Configuration_Guide) at github. Please don’t edit this page as changes will be discarded.
This page provides a comprehensive reference guide for configuring JBrowse. If you find something that is missing or inaccurate, please feel very free to edit it!
Note: this is a reference guide. It is not meant to be read from beginning to end. If this is your first time setting up JBrowse, you probably want to read the Quick-start tutorial first, and then consult this guide when you need information on specific things you want to do with your JBrowse.
Check out the new JBrowse FAQ page for more tips on setup and configuration
Also see the JBrowse Desktop guide here
At the most basic level, setting up JBrowse consists of:
/var/www by default)Both the JBrowse code and these data files must be in a location where the web server can serve them to users. Then, a user pointing their web browser at the appropriate URL for the index.html file in the JBrowse directory will see the JBrowse interface, including sequence and feature tracks reflecting the data source.
Reference sequence data should be added first (using
prepare-refseqs.pl`), followed by annotation data. Once all of
annotation data has been added, use generate-names.pl to make the
feature names searchable.
0. Install build prerequisites, plus make and a C compiler. On Ubuntu, you could do this with:
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
Some other things that sometimes need to be manually installed if your setup.sh is failing includes these
sudo apt-get install libexpat-dev libxml2-dev libdb-dev
If you need a web server you can add apache2 to the list
1. Download JBrowse onto your web server.
2. Unpack JBrowse into a directory that is served by your web browser.
On many systems, this defaults to /var/www or /var/www/html for
apache2
cd /var/www/html
unzip JBrowse-*.zip
Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.
3. Run the automated-setup script, ./setup.sh, which will attempt to
install all of JBrowse’s (modest) prerequisites for you in the
jbrowse/ directory itself. Note that setup.sh should not be run as
root or with sudo.
4. Visit http://your.machine.address/jbrowse/index.html?data=sample_data/json/volvox. If you can see the included Volvox example data, you are ready to configure JBrowse to show your own data! The Getting Started with JBrowse Tutorial provides a very basic step-by-step guide to formatting your own data, and in-depth configuration reference information can be found on this page.
Note: if there is an error installing the perl pre-requisites, and you get an error in your setup.log such as “/home.local/username/.cpanm/build.log: No such file or directory at /loader/0x10b108f0/App/cpanminus/script.pm line 224.”
Then you can clear out your users locallib with rm -rf ~/.cpanm and
re-run setup.sh. Only do this if you are not concerned about your
personal cpanm folder in the first place. Otherwise, you can use your
system’s cpanm to install jbrowse pre-requisites with “cpanm .” inside
the jbrowse directory.
To upgrade an existing JBrowse (1.3.0 or later) to the latest version,
simply move its data directory (and jbrowse_conf.json if you are using
it) into the directory of a newer JBrowse, and the new JBrowse will
display that data.
To upgrade a 1.2.x JBrowse, copy its data directory into the new JBrowse directory, and point your browser at compat_121.html in the new JBrowse directory, instead of index.html. Or, if desired, you could simply overwrite index.html with compat_121.html.
If you are upgrading from a version of JBrowse older than 1.2.0, a fresh installation is required.
JBrowse supports two configuration formats, a JSON-based format and a GBrowse-like textual format that is easier to edit and maintain by hand than JSON. Sites can use either format, or a mixture of both. The default shipped configuration of JBrowse uses both: jbrowse.conf in the main JBrowse directory for global settings, and trackList.json in each data directory for dataset-specific configuration in JSON, and tracks.conf in the data directory for dataset-specific configuration in .conf format.
The JSON configuration format was the first format supported by JBrowse, and is easy for software programs to read and modify. Before version 1.11.0, this was the only format supported by JBrowse.
As an example, the trackList.json file might have something like this. Here is an example of a BAM track
{
"tracks": [
{
"urlTemplate" : "volvox-sorted.bam",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"type" : "JBrowse/View/Track/Alignments2",
"label" : "BAM_track",
"key" : "My BAM track"
"style": { "color": "red" }
}
]
}
The specifics of this config are not essential, we are specifying an array of tracks in a trackList.json style, and each track is an object that includes some parameters like the urlTemplate to refer to the location of the BAM file on the server relative to the data directory, the color of the features, etc.
JBrowse 1.11.0 introduced support for a new text-based configuration format that users of GBrowse will find very familiar, since its design borrows heavily from GBrowse’s configuration syntax. It is fairly comfortable to hand-edit, but rather inconvenient for automated tools to work with. To get the best of both worlds, JBrowse supports both formats.
This text configuration format can be used to specify
The text format has several benefits, including the ability to specify multi-line callbacks. Example:
# BAM track with a new callback
[tracks.mytrack]
storeClass = JBrowse/Store/SeqFeature/BAM
type = JBrowse/View/Track/Alignments2
urlTemplate = myfile.bam
key = My BAM track
style.color = function(feature) {
/* comment */
return 'red';
}
[trackMetadata]
sources =
+ data/mymeta.csv
+ data/more_meta.csv
When your web browser loads a page containing JBrowse, and JBrowse starts, the following steps are done
This is how you eventually get the trackList.json and tracks.conf files from your data directory loaded. Note that the &data=blah URL parameter becomes the dataRoot config parameter, so dataRoot would be “blah” in that case.
The configuration system then merges all this information, e.g. from the URL params, from the Browser constructors, the defaultConfigs, the jbrowse.conf, the jbrowse_conf.json, the trackList.json, the tracks.conf, and any files that the trackList.json or tracks.conf files themselves include, into a single config.
Generally this happens all seamlessly, and both the text-based .conf format and .json config files can co-exist. That is because anything that can be written as a .conf file can also be written as a .json, they are both parsed on the client side into config objects.
The reference sequences on which the browser will display annotations, and which provide a common coordinate system for all tracks. At a close enough zoom level, the sequence bases are visible in the “Reference Sequence” track.
The exact interpretation of “reference sequence” will depend on how you are using JBrowse. For a model organism genome database, each reference sequence would typically represent a chromosome or a contig. Before any feature or image tracks can be displayed in JBrowse, the reference sequences must be defined using the prepare-refseqs.pl formatting tool.
JBrowse displays a dropdown selector for changing reference sequences.
For JBrowse versions 1.6.3 to 1.8.1, if more than 30 reference sequences
are loaded, this selector is not shown by default. To force JBrowse to
show the reference sequence dropdown selector, set
refSeqDropdown: true in the configuration. This can be done in any
configuration file, e.g. index.html, jbrowse_conf.json, or
data/trackList.json.
In JBrowse version 1.9.0 and later, the reference sequence dropdown menu
is always displayed. However, if there are too many reference sequences
to practically display in the dropdown selector, the first portion of
the sequence list is shown in the dropdown selector, along with a
message stating that there are more reference sequences than can be
shown. The maximum number of reference sequences in the selector is set
by the refSeqSelectorMaxSize configuration variable, and defaults to 30.
The ordering of reference sequences in the selector is configurable
using the refSeqOrder configuration variable.
Supported values for refSeqOrder include
namename descendinglengthlength descendingfalse/null/0 to disable any sortingby_list to manually specify a list of reference sequences in the
selectorOne instance in which refSeqOrder is particularly useful is in
displaying annotations on early-stage, incomplete genomic assemblies: to
display the N biggest contigs in the assembly in the reference sequence
selector dropdown, one can set refSeqOrder to ‘length descending’, and
set refSeqSelectorMaxSize to N.
If you set refSeqOrder to by_list, you can then set
refSeqOrderList to set the exact order of the reference sequence list.
Example (in data/tracks.conf)
[GENERAL]
refSeqOrder = by_list
refSeqOrderList =
+ ctgB
+ ctgA
+ ctgAprime
+ bethsCrazyBananasContig
+ ctgAZed
This script is used to format sequence data for use by JBrowse, and must be run before adding other tracks. In addition to formatting the sequence data, this script creates a track called “DNA” that displays the reference sequence. The simplest way to use it is with the –fasta option, which uses a single sequence or set of reference sequences from a FASTA file:
bin/prepare-refseqs.pl --fasta <fasta file> [options]
If the file has multiple sequences (e.g. multiple chromosomes), each sequence will become a reference sequence by default. You may switch between these sequences by selecting the sequence of interest via the pull-down menu to the right of the large “zoom in” button.
You may use any alphabet you wish for your sequences (i.e., you are not restricted to the nucleotides A, T, C, and G; any alphanumeric character, as well as several other characters, may be used). Hence, it is possible to browse RNA and protein in addition to DNA. However, some characters should be avoided, because they will cause the sequence to “split” - part of the sequence will be cut off and and continue on the next line. These characters are the hyphen and question mark. Unfortunately, this prevents the use of hyphens to represent gaps in a reference sequence.
In addition to reading from a fasta file, prepare-refseqs.pl can read sequences from a gff file or a database. In order to read fasta sequences from a database, a config file must be used.
Syntax used to import sequences from gff files:
bin/prepare-refseqs.pl --gff <gff file with sequence information> [options]
Syntax used to import sequences with a config file:
bin/prepare-refseqs.pl --conf <config file that references a database with sequence information> --[refs|refid] <reference sequences> [options]
Syntax used to import a indexed fasta(i.e. a fasta file where you run `samtools faidx yourfile.fa` which outputs yourfile.fa.fai)
bin/prepare-refseqs.pl --indexed_fasta yourfile.fa
This will copy yourfile.fa and yourfile.fa.fai to the data directory
| Option | Value |
|---|---|
| fasta, indexed_fasta, twobit, gff, sizes, or conf | Path to the file that JBrowse will use to import sequences. With the fasta and gff options, the sequence information is imported directly from the specified file. With the sizes option, a tab delimited file with chromosome names and lengths is used, but no sequence information is added. With the conf option, the specified config file includes the details necessary to access a database that contains the sequence information. Exactly one of these three options must be used. With indexed_fasta, the samtools faidx yourfile.fa must be run before hand. With twobit, the twobit file will automatically be copied into your data directory. |
| out | A path to the output directory (default is ‘data’ in the current directory) |
| seqdir | The directory where the reference sequences are stored (default: <output directory>/seq) |
| noseq | Causes no reference sequence track to be created. This is useful for reducing disk usage. |
| refs | A comma-delimited list of the names of sequences to be imported as reference sequences. This option (or refid) is required when using the conf option. It is not required when the fasta or gff options are used, but it can be useful with these options, since it can be used to select which sequences JBrowse will import. |
| refids | A comma-delimited list of the database identifiers of sequences to be imported as reference sequences. This option is useful when working with a Chado database that contains data from multiple different species, and those species have at least one chromosome with the same name (e.g. chrX). In this case, the desired chromosome cannot be uniquely identified by name, so it is instead identified by ID. This ID can be found in the ‘feature_id’ column of ‘feature’ table in a Chado database. |
Note: the `prepare-refseqs.pl –sizes chrom.sizes` option is maybe underappreciated. You can technically run jbrowse without any sequence data loaded, simply a set of chromosomes and their sizes. The chrom.sizes file simply can contain two column tab seperated list of chromosome names and their lengths.
JBrowse has several different tools that can be used to convert
range-based annotation data (genes, transcripts, etc) to range-indexed
sets of static JSON files that are very fast for JBrowse to access. Each
of these tools also adds a track configuration stanza to the
trackList.json configuration file in its output directory.
Each run of this script formats a single track for JBrowse. A flat file is a data set that exists entirely in a single file. For this script, the file must be a GFF3, BED, or GenBank text file.
Basic usage:
bin/flatfile-to-json.pl --[gff|gbk|bed] <flat file> --tracklabel <track name> [options]
For a full list of the options supported by flatfile-to-json.pl, run it with the –help option
bin/flatfile-to-json.pl --help
Example
flatfile-to-json.pl \
( --gff <GFF3 file> | --bed <BED file> | --gbk <GenBank file> ) \
--trackLabel <track identifier> \
[ --trackType <JS Class> ] \
[ --out <output directory> ] \
[ --key <human-readable track name> ] \
[ --className <CSS class name for displaying features> ] \
[ --urltemplate "http://example.com/idlookup?id={id}" ] \
[ --arrowheadClass <CSS class> ] \
[ --noSubfeatures ] \
[ --subfeatureClasses '{ JSON-format subfeature class map }' ] \
[ --clientConfig '{ JSON-format style configuration for this track }' ] \
[ --config '{ JSON-format extra configuration for this track }' ] \
[ --thinType <BAM -thin_type> ] \
[ --thicktype <BAM -thick_type>] \
[ --type <feature types to process> ] \
[ --nclChunk <chunk size for generated NCLs> ] \
[ --compress ] \
[ --sortMem <memory in bytes to use for sorting> ] \
[ --maxLookback <maximum number of features to buffer in gff3 files> ] \
[ --nameAttributes "name,alias,id" ] \
The –trackLabel parameter is the only required parameter, and is the “id” to refer to your track by. The displayed name is also whatever –trackLabel is unless –key is specified, in which case, whatever –key is will be used as the displayed name.
By default the output is in a folder called data in your current working directory, or whatever is specified by –out
Using –trackType CanvasFeatures is generally useful since CanvasFeatures are newer than the default HTMLFeatures (aka FeatureTrack)
This script uses a config file to produce a set of feature tracks in JBrowse. It can be used to obtain information from any database with appropriate schema, or from flat files. Because it can produce several feature tracks in a single execution, it is useful for large-scale feature data entry into JBrowse.
Basic usage:
bin/biodb-to-json.pl --conf <config file> [options]
For a full list of the options supported by biodb-to-json.pl, run it with the –help option, like:
bin/biodb-to-json.pl --help
This script uses data from a local dump of the UCSC genome annotation MySQL database. To reach this data, go to hgdownload.cse.ucsc.edu and click the link for the genome of interest. Next, click the “Annotation Database” link. The data relevant to ucsc-to-json.pl (*.sql and *.txt.gz files) can be downloaded from either this page or the FTP server described on this page.
Together, a *.sql and *.txt.gz pair of files (such as cytoBandIdeo.txt.gz and cytoBandIdeo.sql) constitute a database table. Ucsc-to-json.pl uses the *.sql file to get the column labels, and it uses the *.txt.gz file to get the data for each row of the table. For the example pair of files above, the name of the database table is “cytoBandIdeo”. This will become the name of the JBrowse track that is produced from the data in the table.
In addition to all of the feature-containing tables that you want to use as JBrowse tracks, you will also need to download the trackDb.sql and trackDb.txt.gz files for the organism of interest.
Basic usage:
bin/ucsc-to-json.pl --in <directory with files from UCSC> --track <database table name> [options]
Hint: If you’re using this approach, it might be convenient to also download the sequence(s) from UCSC. These are usually available from the “Data set by chromosome” link for the particular genome or from the FTP server.
For a full list of the options supported by ucsc-to-json.pl, run it with the –help option, like:
bin/ucsc-to-json.pl --help
Feature tracks can be used to visualize localized annotations on a sequence, such as gene models, transcript alignments, SNPs and so forth.
JBrowse HTMLFeatures tracks, the default legacy track type for range-based features, have many available options for customization, not all of which are available from the command-line formatting scripts. Below is a comprehensive list of configuration options for HTMLFeatures tracks. HTMLFeatures tracks are also referred to as trackType: “FeatureTrack” or “type”: “FeatureTrack”.
| Option | Value |
|---|---|
yScalePosition |
Position of the y-axis scale indicator when the track is zoomed far enough out that density histograms are displayed. Can be “left”, “right”, or “center”. Defaults to “center”. |
maxFeatureScreenDensity |
Maximum density of features to display on the screen. If this is exceeded, will display either feature density histograms (if available), or a “too many features to show” message. The units of this number are features per screen width in pixels. Defaults to 0.5. |
description |
Comma-separated list of fields in which to look for the description of a feature. Case-insensitive. If set to false or null, no feature description will be shown. Defaults to ‘note, description’. |
maxDescriptionLength |
Maximum length, in characters, for displayed feature descriptions. |
minSubfeatureWidth |
Minimum width, in pixels, of the top-level feature for JBrowse to attempt to display its subfeatures. Default 6. |
menuTemplate |
Optional menu configuration for right-click menus on features. Can be as large and complicated as you want. See #Customizing_Right-click_Context_Menus below. If set to null or false, disables feature right-click menus. |
hooks→create |
JavaScript function that creates the parent feature HTML element and returns it. By default this is: function(track,feature) { return document.createElement('div'); }, which creates an HTML div element. |
hooks→modify |
JavaScript function that can be used to modify the feature HTML element in any way desired. If set, the function is called with the track object, feature object, and feature HTML element as arguments (signature: function(track, feature, featDiv)). |
style→featureScale |
Minimum zoom scale (pixels/basepair) for displaying individual features in the track. Not set by default, and overrides the maxFeatureScreenDensity. |
style→className |
CSS class for parent features. Defaults to “feature”. |
style→subfeatureClasses |
Key-value pairs of CSS classes for subfeatures, organized by feature type. Example: { “CDS” : “transcript-CDS”,”UTR” : “transcript-UTR” } |
style→featureCss |
Text string of additional CSS rules to add to features. Example: “border-color: purple; background-color: yellow;” |
style→arrowheadClass |
CSS class of the strand arrowheads to show for this feature. Defaults to ‘arrowhead’. If set to null, no arrowhead will be drawn. |
style→histScale |
Scale (pixels per basepair) below which the track will attempt to draw feature density histograms instead of features, if available. By default, this is set to 4 times the average feature density (features per basepair) of the track. |
style→label |
Comma-separated list of case-insensitive feature tags to use for showing the feature’s label. The first one found will be used. Default ‘name,id’. |
style→labelScale |
Scale (pixels per basepair) above which feature labels (names) will be shown. By default, this is set to 30 times the average feature density (features per basepair) of the track. |
style→descriptionScale |
Scale (pixels per basepair) above which long feature descriptions will be shown. By default, this is set to 170 times the average feature density (features per basepair) of the track. |
style→description |
Comma-separated list of case-insensitive feature tags to check for the feature’s long description. The first one found will be used. Default ‘note,description’. If blank no description is used. |
style→showLabels |
If set to true, feature labels may be shown. Defaults to true. Set this to false to disable display of feature labels. |
maxHeight |
Maximum height, in pixels, that the track is allowed to grow to. When it reaches this height, features that stack higher than this will not be shown, and a “Max height reached” message will be displayed. Default 600 pixels. |
showNoteInAttributes |
If set to true, show the feature’s “Note” attribute as a regular attribute in the feature detail dialog. This is mostly useful for projects that want the blue description text on a feature to be different from the feature’s Notes attribute, but still display the Notes attribute in the detail dialog |
topLevelFeatures |
Specifies which feature types should be considered “top-level” for this track. For example, if you have a track with gene->mRNA->CDS features, but for some reason want to only display the mRNA features, you can set topLevelFeatures=mRNA. Can also be an array of string types, or a function callback that returns an array of types. Default: all features are displayed. Added in 1.14.0 |
HTMLFeatures track configuration options
Introduced in JBrowse 1.10.0, the new JBrowse CanvasFeatures tracks are faster and easier to configure than HTMLFeatures tracks.
| Option | Description |
|---|---|
maxHeight |
Maximum height, in pixels, that the track is allowed to grow to. When it reaches this height, features that stack higher than this will not be shown, and a “Max height reached” message will be displayed. Default 600 pixels. |
style→showLabels |
If true, allows feature labels to be shown if features are not too dense on the screen. Default true. |
style→showTooltips |
If true, allows feature name tooltips to be shown. Default true. |
displayMode |
‘normal’, ‘compact’, or ‘collapsed’. Sets the initial display mode of the track. Default ‘normal’. |
style→featureScale |
Minimum zoom scale (pixels/basepair) for displaying individual features in the track. Not set by default, and overrides the maxFeatureScreenDensity. |
maxFeatureScreenDensity |
Maximum density of features to display on the screen. If this is exceeded, will display either feature density histograms (if available), or a “too many features to show” or “too much data to show” message. The units of this number are features per screen width in pixels. Defaults to 0.5. If increased to ~6 then it should pretty much always go away |
glyph |
JS class name of the glyph to use for each feature. By default, it tries to guess for each feature based on its type attribute, and uses JBrowse/View/FeatureGlyph/Box if it cannot find something better. Can be a callback with signature (feature), returning a string class name. |
menuTemplate |
Optional menu configuration for right-click menus on features. Can be as large and complicated as you want. See #Right-click_Context_Menus below. If set to null or false, disables feature right-click menus. |
style→maxDescriptionLength |
Maximum length, in characters, of long feature descriptions, for glyphs that support them. Default 70. |
style→color |
Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default ‘goldenrod’. | |
style→mouseovercolor |
Color of the overlay drawn on top of features when the mouse hovers over them. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default rgba(0,0,0,0.3), which is semi-transparent black. | |
style→borderColor |
Color of the borders drawn around boxes in glyphs. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default varies from glyph to glyph. | |
style→borderWidth |
Width of the borders drawn around boxes in glyphs. Default 0.5 if borderColor specified |
style→height |
Height in pixels of glyphs. Default value varies from glyph to glyph. |
style→marginBottom |
Margin space to leave below each feature when arranging them in the view. Default 2 pixels. |
style→strandArrow |
If true, allow glyphs to draw strand arrowheads on features that are stranded. Default true. |
style→label |
Comma-separated list of case-insensitive feature tags to use for showing the feature’s label. The first one found will be used. Default ‘name,id’. |
style→textFont |
Font used for feature labels. Same format as CSS font rules. Default ‘normal 12px Univers,Helvetica,Arial,sans-serif’. |
style→textColor |
Color of feature labels. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default ‘black’. | |
style→text2Color |
Color of feature descriptions. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default ‘blue’. | |
style→text2Font |
Font used for feature descriptions. Same format as CSS font rules. Default ‘normal 12px Univers,Helvetica,Arial,sans-serif’. |
style→description |
Comma-separated list of case-insensitive feature tags to check for the feature’s long description. The first one found will be used. Default ‘note,description’. If blank no description is used. |
style→connectorColor |
Color of the connecting line drawn between boxes in glyphs that draw segments (like the Segments, ProcessedTranscript, and Gene glyphs). Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default ‘#333’. | |
style→connectorThickness |
Thickness in pixels of the connecting line drawn between boxes in glyphs that draw segments (like the Segments, ProcessedTranscript, and Gene glyphs). Default 1. |
style→utrColor |
Color of UTR regions drawn by ProcessedTranscript and Gene glyphs. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Defaults to be a color that complements the current style→color value (calculated using a bit of color theory). |
|
subParts |
Comma-separated list of feature type tags that will be drawn as subparts of parent features. Defaults to all features for Segments glyphs, and ‘CDS, UTR, five_prime_UTR, three_prime_UTR’ for ProcessedTranscript glyphs. |
transcriptType |
For Gene glyphs, the feature type tag that indicates that a subfeature is a processed transcript. Defaults to ‘mRNA’. |
labelTranscripts |
For Gene glyphs, if true, draw a label with the transcript’s name beside each transcript, if space permits. Default true. |
style→transcriptLabelColor |
For Gene glyphs, the color of transcript name labels. Color syntax is the same as that used for CSS, specified at <a href=”http://dev.w3.org/csswg/css-color/” class=”external free” |
| rel=”nofollow”>http://dev.w3.org/csswg/css-color/</a>. Default ‘black’. | |
style→transcriptLabelFont |
For Gene glyphs, the font used for transcript name labels. Same format as CSS font rules. Default ‘normal 10px Univers,Helvetica,Arial,sans-serif’. |
impliedUTRs |
Introduced in JBrowse 1.10.5. If true, indicates that UTRs are not present in the feature data, but should be inferred from the overlap of exon and CDS features in ProcessedTranscript and Gene glyphs. Default false. Can be a callback. |
maxFeatureGlyphExpansion |
A factor to expand the glyphs by so that if subfeatures go outside the bounds of the parent feature, they will still be rendered. Default: 500bp/current scale. |
inferCdsParts |
If a single CDS span covers the whole gene except the UTRs, then it is drawn as though it only covers the exon parts (not the introns). Default: false. Added in 1.12.3 |
disableCollapsedClick |
Disables the click action when track is collapsed. Default: false. Added in 1.13.0 |
enableCollapsedMouseover |
Enables the mouseover action when track is collapsed. Default: false. Added in 1.13.0. See the ChromHMM track in volvox sample browser for example of mouseover on the collapsed track |
topLevelFeatures |
Specifies which feature types should be considered “top-level” for this track. For example, if you have a track with gene->mRNA->CDS features, but for some reason want to only display the mRNA features, you can set topLevelFeatures=mRNA. Can also be an array of string types, or a function callback that returns an array of types. Default: all features are displayed. Added in 1.14.0 |
ItemRgb |
If set to true, the RGB colors specified in BigBed or BED files will be used for the feature’s background color. Default true. Added in 1.14.0 |
CanvasFeatures track configuration options
Note: the “compact” displayMode for CanvasFeatures tracks uses style->height and multiplies it by 0.35 to create the compact view. Therefore, if you adjust style->height to a smaller default value, then you can create “ultra compact” visualizations.
Unlike HTML-based feature tracks, canvas-based feature tracks don’t use
modify and create hooks. Instead, the glyph variable, and all of the
style variables, support customization callbacks.
All style callbacks are like:
function( featureObject, variableName, glyphObject, trackObject ) { return '#ffcccc'; }
And the glyph callback is like:
function( featureObject ) { return 'JBrowse/View/FeatureGlyph/<glyphclassname>'; }
So, for example, if you wanted to customize a CanvasVariants track to color all homozygous variants blue, and all heterozygous variants red, you could set something like:
[tracks.myvcf]
...
variantIsHeterozygous = function( feature ) {
var genotypes = feature.get('genotypes');
for( var sampleName in genotypes ) {
try {
var gtString = genotypes[sampleName].GT.values[0];
if( ! /^1([\|\/]1)*$/.test( gtString) && ! /^0([\|\/]0)*$/.test( gtString ) )
return true;
} catch(e) {}
}
return false;
}
style.color = function( feature, variableName, glyphObject, track ) {
return track.config.variantIsHeterozygous(feature) ? 'red' : 'blue';
}
Note: the multiline callbacks are only enabled in the tracks.conf form. See Text Configuration Format (.conf) for more considerations about this format.
| Option | Description |
|---|---|
subfeatureDetailLevel |
Set the level of detail of the View details box. If set to 1, only displays one level of subfeatures for example. Default: 0 which displays all subfeature levels. Added in 1.12.3 |
Generic track configuration options
Starting in JBrowse version 1.11.3, the ability to customize parts of the ‘View details’ Pop-ups was added. This lets you specify functions that have the format fmtDetailValue_* or fmtDetailField_* to either change the value section of an attribute in the config, or the fieldname of an attribute in the config.
Here is an example in tracks.conf format for formatting the “Name” field by adding a link to it:
[tracks.mygff]
key = My Gene Track
storeClass = JBrowse/Store/SeqFeature/NCList
type = FeatureTrack
fmtDetailValue_Name = function(name) {
return "<a href='http://www.example.com?featurename="+name+"'>"+name+"</a>";
}
Note: It is also easy to specify these methods in trackList.json format.
{
"key": "My Gene Track",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"type" : "FeatureTrack",
"label": "mygff",
"fmtDetailValue_Name": "function(name) { return '<a href=\"http://www.example.com?featurename='+name+'\">'+name+'</a>'; }"
}
Addendum: If the field has multiple values (e.g. multiple DBXrefs or GO terms), then the callback will receive an array as it’s argument, and then you can also return an array which indicates that each element will be formatted inside its own \ In this case you will check that the input is an array, because it will also be called on the individual elements too. For example
"fmtDetailValue_links": "function(links) { if(Array.isArray(links)) { return links; } else return `<a href=\"${link}\">${link}</a>`; }"
This shows that you could, in essence, pre-process the array if you wanted, but the same callback is then called on the individual elements, so you handle both these cases.
In JBrowse 1.11.5, some additional customizations to the pop-up boxes were added.
1. The ability to access the feature data was added to the callback signature of the fmtDetailValue_* functions. Example:
fmtDetailValue_Name = function(name, feature) {
/* only add links to the top-level feature */
if(feature.get('type')=='mRNA') {
return name + ' [<a href=http://www.ncbi.nlm.nih.gov/gquery/?term='+name+'>Search NCBI</a>]';
}
}
2. The ability to customize the ‘About track’ popups was added. These callbacks are named fmtMetaValue_* and fmtMetaField_*
3. The ability to customize mouseover descriptions of the fieldnames was also added. These callbacks are named fmtDetailDescription_* and fmtMetaDescription_*
4. The ability to remove a field from the popup was added. You can do this by returning null from a fmtDetailField_* and fmtMetaField_* callback;
Beginning with JBrowse 1.5.0, the left-clicking behavior of feature tracks (both HTMLFeatures and CanvasFeatures) is highly configurable. To make something happen when left-clicking features on a track, add an onClick option to the feature track’s configuration.
In the example configuration below, left-clicks on features will open an embedded popup window showing the results of searching for that feature’s name in NCBI’s global search, and “search at NCBI” will show in a tooltip when the user hovers over a feature with the mouse:
"tracks": [
{
"label" : "ReadingFrame",
"category" : "Genes",
"class" : "dblhelix",
"key" : "Frame usage",
"onClick" : {
"label": "search at NCBI",
"url": "http://www.ncbi.nlm.nih.gov/gquery/?term={name}"
}
}
...
For details on all the options supported by onClick, see Click Configuration Options.
Note: the style→linkTemplate variable can also be used to specify a URL for left-click on features, but this is a legacy option.
The onClick->label attribute from the previous section is used as the mouse-over description for features on the HTMLFeatures and CanvasFeatures tracks.
In JBrowse 1.11.6, the onClick->label attribute was extended further to allow the mouse-over description to be customized using callbacks and template strings.
Example for CanvasFeatures, allows full HTML tooltips. Here the {name} template is automatically filled in with the feature info:
"onClick": {
"label" : "Feature name: {name}",
"title" : "{name} {type}",
"action": "defaultDialog"
}
Example for HTMLFeatures, which only allows plain text descriptions but can support newlines (essentially uses \ for mouseover).
"onClick": {
"label": "Feature name {name}\nFeature start {start}\nFeature end {end}",
"title" : "{name} {type}",
"action": "defaultDialog"
}
Example using a callback (for either HMTLFeatures or CanvasFeatures), using this.feature to access the feature details
"onClick": {
"label": "function() { return 'Feature name: '+this.feature.get('name'); }",
"title" : "{name} {type}",
"action": "defaultDialog"
}
Note: on CanvasFeatures, the action “defaultDialog” isn’t necessary, but it is necessary for HTMLFeatures to keep the default dialog (as of writing, 1.11.6).
Also note: The “label” which is used in the text for mouseover will be used for the title of any popup by default, so you might also specify a different title.
Also also note: Your mouseover will crash if your features do not have an ID or name, even if you coded the mouseover to not use ID or name.
Canvas-based feature tracks (CanvasFeatures) support an optional
histograms configuration subsection that can contain a definition for
a second datastore that holds quantitative data (usually either coverage
depth or feature density) to be displayed when zoomed further out than
featureScale (or if featureScale is not set, the scale determined by
the store’s feature density divided by maxFeatureScreenDensity). This
is often used for BAM coverage on Alignments2 tracks using the
histograms.urlTemplate and histograms.storeClass arguments.
Example track
[ tracks.mytrack ]
histograms.storeClass = JBrowse/Store/SeqFeature/BigWig
histograms.urlTemplate = coverage.bw
storeClass = JBrowse/Store/SeqFeature/BAM
urlTemplate = file.bam
type = Alignments2
Feature tracks can be configured to display a context menu of options when a user right-clicks a feature item. Here is an example of a track configured with a multi-level right-click context menu:
{
"feature" : [
"match"
],
"track" : "Alignments",
"category" : "Alignments",
"class" : "feature4",
"key" : "Example alignments",
"hooks": {
"modify": "function( track, feature, div ) { div.style.height = (Math.random()*10+8)+'px'; div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()*5)];}"
},
"menuTemplate" : [
{
"label" : "Item with submenu",
# hello this is a comment
"children" : [
{
"label" : "Check gene on databases",
"children" : [
{
"label" : "Query trin for {name}",
"iconClass" : "dijitIconBookmark",
"action": "newWindow",
"url" : "http://wiki.trin.org.au/{name}-{start}-{end}"
},
{
"label" : "Query example.com for {name}",
"iconClass" : "dijitIconSearch",
"url" : "http://example.com/{name}-{start}-{end}"
}
]
},
{ "label" : "2nd child of demo" },
{ "label" : "3rd child: this is a track" }
]
},
{
"label" : "Open example.com in an iframe popup",
"title" : "The magnificent example.com (feature {name})",
"iconClass" : "dijitIconDatabase",
"action": "iframeDialog",
"url" : "http://www.example.com?featurename={name}"
},
{
"label" : "Open popup with XHR HTML snippet (btw this is feature {name})",
"title": "function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }",
"iconClass" : "dijitIconDatabase",
"action": "xhrDialog",
"url" : "sample_data/test_snippet.html?featurename={name}:{start}-{end}"
},
{
"label" : "Open popup with content snippet (btw this is feature {name})",
"title": "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }",
"iconClass" : "dijitIconDatabase",
"action": "contentDialog",
"content" : "function(track,feature,div) { return '<h2>{name}</h2><p>This is some test content about feature {name}!</p><p>This message brought to you by the number <span style=\"font-size: 300%\">'+Math.round(Math.random()*100)+'</span>.</p>
},
{
"label" : "function(track,feature,div) { return 'Run a JS callback '+Math.random()+' title!'; }",
"iconClass" : "dijitIconDatabase",
"action": "function( evt ){ alert('Hi there! Ran the callback on feature '+this.feature.get('name')); }"
},
{
"label": "Create a url with a callback",
"action": "iframeDialog",
"iconClass": "dijitIconDatabase",
"title": "Create a url with a callback",
"url": "function(track,feature) { return
'http://www.example.com?refseq='+track.refSeq.name
+'&featurename='+feature.get('name')+'&start='+feature.get('start')+'&end='+feature.get('end'); }"
},
]
}
This configuration results in a context menu like the one pictured below. For details on what each of the options supported by menu items does, see #Click Configuration Options.
The Google Chrome headless browser “Puppeteer” is an alternative to PhantomJS
The jbrowse-rasterize tool from cpgJBrowseToolkit provides a tool for automating puppeteer https://github.com/cancerit/cgpJBrowseToolkit/
A stripped down puppeteer example is as follows
First run “npm install puppeteer” in a new directory, then create a file screenshot.js
const puppeteer = require('puppeteer');
function delay(ms) {
return new Promise(r => setTimeout(r, ms));
}
(async () => {
const browser = await puppeteer.launch();
const page = await browser.newPage();
const argv=process.argv;
await page.goto(argv[2]);
//debug
//page.on('console', msg => console.log('PAGE LOG:', msg.text()));
await page.setViewport({
width:+argv[4]||1000,
height:+argv[5]||600,
deviceScaleFactor:argv[6]||2
});
// wait five seconds for rendering, add or remove time as needed
await delay(5000);
await page.screenshot({path: argv[3]||"example.png"});
await browser.close();
})();
Then you can run “node screenshot.js http://localhost/jbrowse/” or other URL argument as needed. The third, fourth, fifth and sixth arguments are optional a) output filename b) output width c) output height and d) zoom factor to make it higher resolution