[Jalview-discuss] unable to create png image from alignment

[Jim Procter]

Hello there, Ali.

On 09/02/2010 16:48, Ffenics wrote:
>
> 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
>
> Jalview -open /my_dir/myfile..fa -dasserver das1=http://mydas1url 
> -dasserver das2=http://mydas2url -png myalignment.png
>
> But the .png file s not being created. The alignment itself opens up 
> fine as do the DAS connections.

Well spotted! The command line das annotation retrieval mechanism has 
not been well tested, so your post was a really useful bug report. This 
problem has now been fixed in the development version (launch/download 
from www.jalview.org/versions.html).

Thanks..
Jim.

ps. with regard to the other bug report regarding the 2.4.0b2 version 
that you sent in - please let me know if you experience similar problems 
with the latest development version.. it may be a java runtime issue.

-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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