GBrowse Configuration/Images

This article describes static images and how to create them in GBrowse.

For the main GBrowse configuration article, see:

Generating Static Images: PNGs, SVGs and PDFs

GBrowse can create three types of static image suitable for incorporation into posters, publications or other web pages:

All the work is handled by the gbrowse_img script and needs little configuration. When the user selects a region and set of tracks to browse, the “link to image” and “high-res image” links at the top of the page will be automatically set to reproduce the user’s view as closely as possible. GBrowse_img customization options, including instructions on how to embed an image in a web page so that the clickable imagemap links are maintained, can be found here.

The PNG generation will work in the default installation. In order to get SVG generation to work, you will need to install the perl SVG and GD::SVG modules, available from CPAN.

For PDF generation, you will need the perl GD and GD::SVG modules installed, as well as a helper application called Inkscape. Inkscape provies a command-line tool that will convert SVG files into PDF. To install, download and install it somewhere on the standard system path (e.g. /usr/bin). You will then need to create two subdirectories in the web user’s home directory in order for inkscape to work properly. Assuming that the web user is “www-data” run the following commands:

sudo mkdir ~www-data/{.inkscape,.gnome2}
sudo chown www-data ~www-data/{.inkscape,.gnome2}

This will create the two directories “.inkscape” and “.gnome2” in the www-data user’s home directory, and make them writable by the www-data user.

Unfortunately, Inkscape will generate a one line warning into the server error log every time it executes:

(inkscape:28490): Gdk-CRITICAL **: gdk_display_list_devices: assertion `GDK_IS_DISPLAY (display)' failed

At the current time there is no known fix for this problem.

Note that Inkscape PDF generation should work properly on all platforms, including Linux, Mac OSX and Windows. However, it has only been tested on Linux platforms at the current time.