I’m currently investigating how to run Jalview on the command line. I’m opening up a fasta alignment, connecting to a couple of das servers and then trying to output the alignment as a png file.
This is what I’m adding to the command line
But the .png file s not being created. The alignment itself opens up fine as do the DAS connections.
The output.txt says:
Java version: 1.6.0_13
amd64 Linux 2.6.18-128.1.6.el5
Jalview Version: Automated Build
INFO - Not enabling Google Tracking.
I’m running the InstallAnywhere installation from October last year.
Any help much appreciated!!!