[EMBOSS] Handling of local file input in Jemboss

[Rozenbaum, Daniel (Biocceleration Inc)]

Hi Mahmut,

I just noticed that the most recent changes might have introduced the following glitch: server side directories for Jemboss jobs on the server now appear to be created under the path that is a concatenation of paths "results.home" and "embossBin" in jemboss.properties. In other words if results.home is /path/to/emboss_results/ and embossBin is /usr/local/emboss/6.4.0/bin/ , I'm now getting Jemboss job directories created under /path/to/emboss_results/usr/local/emboss/6.4.0/bin/ .

Could you please let me know if you're able to repdocude this?

Many thanks,
Daniel

________________________________________
From: Mahmut Uludag [uludag at ebi.ac.uk]
Sent: Friday, September 21, 2012 7:07 AM
To: Rozenbaum, Daniel (Biocceleration Inc)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] Handling of local file input in Jemboss

Hi Daniel,

> supplying a remote file as input no longer works, and neither
> does using list files (either local or remote).
>
> When I try to use a local list file, the file does make it to server
> side, but the command line appearing in .desc doesn't have the '@'
> before the file name, and that seems to be the reason for the job
> failure.
>
> When I try to use a remote file, the generated command line doesn't
> contain a reference to the input file at all, and the resultant error
> message reads "Error: Unable to read sequence '' ".
>
> Can you reproduce these, or did I mess something up during my attempt
> to apply the patch and reinstall?

It was my mistake, apologies. When I initially looked to the problem I
noticed possible changes may include/interfere-with handling of
list-files and remote-files but in my last look I just forgot this point.

I now have tried fixing it but this has required some changes on the
server side as well. Can you download latest versions of the following
two files and test again.

http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java?view=log

http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/server/JembossServer.java?view=log

(These 2 files has not changed much recently, as far as i can see they
are happy to work as part of 6.4.0)

Regards,
Mahmut