[EMBOSS] Jemboss setup problem

[uludag at ebi.ac.uk]

> But I am not quite there yet. I have two other "problems" and one other
> question. Part of my problem is my lack of familiarity with the GUI
> interface. I have been using EMBOSS on the command line for quite some
> time. Anyway with Jemboss when I run the runJemboss.sh script a little
> box pops up asking for a username and password (it looks like a login
> for a remote server). Do you have any idea what that is for? Do I have
> to comment out something in the runJemboss.sh script to stop it running?

You might have "user.auth=true" in your jemboss.properties file which
might be found in your share/EMBOSS/jemboss/resources/ directory under
your jemboss installation folder or it might be in your home directory.
Setting this property to false may help.

> The other problem I am having is that when I use pepstats on the command
> line on the file at this link:
> https://webspace.uth.tmc.edu/rmackenzie/public/orf_trans_all_assembly_21
> .fasta
> I get a result in about 2 seconds. But when I try doing this through
> Jemboss it just sits there with the hourglass going.
> I have also tried this using the windows XP version of Jemboss, running
> on my dual core 2 Gb of RAM PC at my house. I ran it for 12 hours and
> still go no output. If you have a Jemboss running there could you try
> running the file through pepstats for me? I think it is a bug and if so
> I should report it. By the way I tried stripping out the * for the stop
> codons but it made no difference.

I'm able to reproduce this problem and will return you tomorrow with more
details. I initially thought giving more memory to Java may help to solve
the problem but it doesn't.

> And the final question. Do other users of this list normally post
> replies to the list?

I think it depends on the post. It is good to post to the list when you
think others may also hit the same problem.

Regards,
Mahmut