[EMBOSS] Handling of local file input in Jemboss

[Rozenbaum, Daniel (Biocceleration Inc)]

Hi everyone,

I'm trying to figure out whether this issue I'm dealing with is a bug in Jemboss or a bug in my understanding :-) .

I have EMBOSS 6.4.0 with Jemboss 1.5 installed in client-server mode. The server is a Linux box, and Jemboss is started via Java Web Start on a Windows box. Then I follow this sequence of steps:

1. Run "makeprotseq" interactively in Jemboss to generate a few random sequences. This works fine. When the "Saved Results" window opens, I use "File --> Save to Local File" to save the result as "C:\TEMP\sequences.fasta"

2. Open "seqret" in Jemboss, and use the "Browse files" option to select "C:\TEMP\sequences.fasta" as input.

3. Run seqret interactively. The Saved Results window that opens contains the following error messages:
Error: Failed to open filename 'C'
Error: Unable to read sequence 'C:\TEMP\sequences.fasta'
Died: seqret terminated: Bad value for '-sequence' with -auto defined
Looking in the subdirectory created for this job on the server side, it does contain a file "C__TEMP__sequences.fasta" with the correct contents. But the ".desc" file in that directory reads the following:
EMBOSS run details

Application: seqret
 -nofeature -sequence C:\TEMP\sequences.fasta -nofirstonly -auto C__TEMP_sequences.fasta
Started at Thu Sep 20 11_15_22 EDT 2012

Input files:
/usr/local/emboss/results/username/seqret_Thu_Sep_20_11_15_22_EDT_2012_1234/C__TEMP_sequences.fasta
It appears therefore that the command line, instead of using the path to the server-side copy of the input file, still uses the path to the file on the client.

Does this make sense? Any advice would be greatly appreciated!

With best regards,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering & Development/ Patent System Division
600 Dulany St.
Alexandria, VA 22314