[Jalview-discuss] problem with fasta files

[James Procter]

Hello Judith.

It sounds like the 2.4 release has caused you a number of problems,which
is a shame. I'm not sure what's going on with your Dock icon - all I can
suggest there is removing and re-pinning the icon. However, as to your
other problem:

Judith Cohn wrote:
> p.s. I have a similar problem with a clean install of the latest version
> of Java 2.4 on Linux.  It works similar to my colleague's copy on Mac
> with Tiger.  I can load fasta files from muscle manually using menu
> option but cannot open them with my script.
The issue is a known one - there seems to be a problem with the jars
generated by InstallAnywhere under the new (well - 6 months old now)
automated build system. I had originally thought it to only really be an
issue on the OSX InstallAnywhere distribution, so its a worry that
you've also noticed it on Linux. On windows, the LaunchAnywhere .exe
file passes command line arguments correctly, so the problem isn't so
serious. However, the workaround for command-line launching on OSX was
to either download the jars for the webstart release
(http://www.jalview.org/webstart/) and use those, or build the jalview
jars using the source distribution.

I'm hoping to put up a bugfix release (2.4.0b2) on www.jalview.org in
the next few weeks. This will use the latest version of InstallAnywhere
to create the local installation distribution, and will - I hope - fix
this particular problem.  I'll let you know directly if this really the
case so you can test on your Mac.

until the next email...
Jim Procter.

-- 
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J. B. Procter  (ENFIN/VAMSAS)  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.