cgpJBrowseToolkit

Contains the script 'jbrowse_rasterize.js', a script to generate images from JBrowse.

• Installation
• Installation with Docker
• Usage
• LICENCE

Installation

Requires a working installation of node and npm. Depending on your operating system, you may also need to install additional pacakages for running chromium. For an out-of-the-box installation, please see installation with Docker.

git clone https://github.com/cancerit/cgpJBrowseToolkit.git; npm install .;

Installation with Docker

For conveniance, a Dockerfile is provided to build an image with all necessary requirements installed.

git clone https://github.com/cancerit/cgpJBrowseToolkit.git; cd cgpJBrowseToolkit.git; docker build --tag cgpjbrowsetoolkit:develop;

Usage

jbrowse_rasterize.js generates screenshots from your JBrowse instance using the URL and a BED file of locations of interest.

``` Usage: jbrowse_rasterize [options]

Generate images against a JBrowse server

Options:

-l, --locs Bed file of locations, see --help -b, --baseUrl [value] URL from pre configured JBrowse webpage, ommit if provided in BED file -w, --width [n] Width of image (default: 600) -i, --imgType [value] Type of image jpeg|pdf|png -o, --outdir [value] Output folder (default: ./) -n, --navOff Remove nav bars -d, --dMode [value] Change default display of alignment tracks [normal|compact|collapsed] --highlight Highlight region (for short events) -q, --quality [n] Image resolution 1,2,3 -z, --zoom [n] Zoom factor (default: 1) -p, --passwdFile [file] User username and password password for httpBasic -t, --timeout [n] For each track allow upto N sec. (default: 10) -v, --version output the version number -h, --help output usage information

Additional information:

Image quality: Best image quality is achieved with pdf, but ~5x larger than png.

Zoom: To allow capturing same region in a wider image as JBrowse has a maximum width per base.

--locs bed file:

Can include comment lines to switch the baseUrl used for the next block of coordinates.

Any comment line will be processed into a dataset ($DS) name and URL. Files generated will be output to a subfolder of the specified --output area as:

$OUTPUT/$DS/$CHR-$START_$END.

FORMAT:

DATASET_NAME URL

CHR START END

DATASET_NAME2 URL

CHR START END ...

Comment/URL separator lines can be space or tab separated elements. BED formatted lines must be tab separated and only have 3 elements. ```

Example: Running with 'baseUrl' option

volvox.bed:

ctgA 17173 23150

bash mkdir -p out; node js/jbrowse_rasterize.js \ --imgType png \ --locs volvox.bed \ --outdir out \ --baseUrl 'http://jbrowse.org/code/JBrowse-1.12.4/?tracks=Transcript%2Cvolvox-sorted_bam_coverage&data=sample_data%2Fjson%2Fvolvox';

Example: Running with embedded URL

volvox_urlEmbedded.bed:

```

EmbeddedUrl http://0.0.0.0:8080/?tracks=DNA%2CTranscript%2Cvolvox-sortedbamcoverage%2Cvolvox-sortedbam&data=sampledata%2Fjson%2Fvolvox

ctgA 17173 23150 ```

bash mkdir -p out; node js/jbrowse_rasterize.js \ --imgType png \ --locs volvox_urlEmbedded.bed \ --outdir out

Example: Running with Docker

See installation with Docker.

bash mkdir -p out; docker run \ --rm \ -v ${PWD}:/home/ubuntu \ --user $(id -u):$(id -g) \ cgpjbrowsetoolkit:develop \ node jbrowse_rasterize.js \ --imgType png \ --locs volvox_urlEmbedded.bed \ --outdir out

HTTP-BASIC Authentication

To use this with a site secured with http_basic (username and password) you will need to provide this in a file whos path is set with the --passwdFile option.

eg. pass.txt

username password

Please set permissions accordingly for this file and preferably delete it after use.

LICENCE

``` Copyright (c) 2016-2023 Genome Research Ltd.

Author: CASM/Cancer IT cgphelp@sanger.ac.uk

This file is part of cgpJBrowseToolkit.

cgpJBrowseToolkit is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’." ```