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 _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss