[Jalview-discuss] Fwd: problem with fasta files

[Judith Cohn]

Begin forwarded message:

> From: Judith Cohn <jcohn at lanl.gov>
> Date: June 10, 2009 1:24:15 PM MDT
> To: James Procter <jimp at 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.
>

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