[EMBOSS] Handling of local file input in Jemboss

[Rozenbaum, Daniel (Biocceleration Inc)]

Hi Mahmut,

I've applied the patch you suggested and it seems to have fixed the problem with supplying local sequence files. However, now it appears that 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?

Many thanks in advance,
Daniel

________________________________________
From: Mahmut Uludag [uludag at ebi.ac.uk]
Sent: Thursday, September 20, 2012 6:00 PM
To: Rozenbaum, Daniel (Biocceleration Inc)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] Handling of local file input in Jemboss

Hi Daniel,

When we were implementing the array representation of command lines we
mistakenly added the input sequence file names to the command line array
prepared on the client side. As you showed in your example these inputs
are added to the command line on the server side using their final file
names.

It looks following changes fixes the problem in my 6.4.0 test server and
current CVS code base client.

Index: org/emboss/jemboss/gui/form/BuildJembossForm.java
===================================================================
RCS file:
/home/repository/emboss/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java,v
retrieving revision 1.113
diff -u -r1.113 BuildJembossForm.java
--- org/emboss/jemboss/gui/form/BuildJembossForm.java    29 Jun 2011
14:12:48 -0000    1.113
+++ org/emboss/jemboss/gui/form/BuildJembossForm.java    20 Sep 2012
21:28:14 -0000
@@ -1113,12 +1113,11 @@

            fn = fn.trim();

-          optionsA.add("-" + val);
-          optionsA.add(fn);
-
            if(withSoap)
              options = filesForSoap(fn,options,val,filesToMove);
            else {
+            optionsA.add("-" + val);
+            optionsA.add(fn);
              fn = addQuote(fn);
              options = options.concat(" -" + val + " " +  fn);
            }

Can you please try applying the above change to your 6.4.0 installation.
In 6.4.0 deleted optionsA.add() lines are the lines 1116 and 1117.

Since jemboss has relatively complex installation mechanism, it might be
easier if you apply this change to a freshly extracted tar ball and make
a new installation. Make sure jawa web start doesn't use the cached
version of the jemboss client but uses the updated version.

Regards,
Mahmut

> 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.
>