problem with fasta files

Jalview Discussion
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Begin forwarded message:

From: Judith Cohn <jcohn@lanl.gov>
Date: June 10, 2009 1:24:15 PM MDT
To: James Procter <jimp@compbio.dundee.ac.uk>
Subject: Re: [Jalview-discuss] problem with fasta files

Thanks. Just for fun, I recompiled the source code and indeed it works (at least when calling Jalview from the classes directory I generated - I have not made a jar file yet).

Judith

On Jun 10, 2009, at 10:18 AM, James Procter wrote:

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.

–

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.