[EMBOSS] Jemboss

[Staffa, Nick (NIH/NIEHS) [C]]

Right now I am most concerned about restriction analysis. This is what
my most favored customers need. There is no meaningful output when doing
remap from Jemboss, whilst there is good output from command line. 
There is hardly any meaningful error message.

Message from Jemboss:

Input: local GCG file (previously converted from Genbank file.
Program: remap with all defaults.
Result: Saved Results window: 3 tabs:
	Filename.remap  shows only the locus name
	C_RestoredFile.....    shows the original sequence file.
	Cmd shows   
remap -sequence C__RestoredFiles_staffa_Desktop_PC_Sequences_hspgk2g.seq
-enzymes all -sitelen 4 -mincuts 1 -maxcuts 2000000000 -nosingle  -blunt
-sticky  -ambiguity  -noplasmid  -commercial  -table 0 -frame 6 -cutlist
-noflatreformat  -limit  -translation  -reverse  -orfminsize 0
-nothreeletter  -nonumber  -width 60 -length 0 -margin 10 -name
-description  -offset 1 -nohtml  -auto

Entering an outputfilename makes no difference; no local output file was
generated.

Selecting a remote file, even fasta, from the File Manager and clicking
on Load Sequence Attributes gives Error Message Sequence Not Found
Check the sequence entered. [OK].   Whereas double clicking on the entry
gives a nice picture of the sequence in Remote File window. 

Using a fasta remote sequence the Saved Results has two tabs:
	EF015887.remap   has only the name of the sequence
	Cmd		contains the command. 
Running command line remap on the same sequence using all defaults gives
a nice output showing many cuts many places.

Using the File Manager to move the same fasta file to local C drive and
running remap.  Clicking Load Sequence Attributes does not give any
error.
The output Saved Results now has 3 tabs, but no real output.






-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk] 
Sent: Thursday, April 24, 2008 3:49 AM
To: Staffa, Nick (NIH/NIEHS) [C]
Cc: emboss at lists.open-bio.org; Wright, Douglas (NIH/NIEHS) [C]
Subject: Re: [EMBOSS] Jemboss

Hi Nick,

Staffa, Nick (NIH/NIEHS) wrote:
> My sysadmin guy installed Jemboss but it doesn't seem to know about
dataset
> and datafiles (like Rebase) .
> Command line emboss does just fine finding stuff like REBASE.

This suggests they are using some different setup. If the database files

were installed in the default directories, and you have only one EMBOSS 
installation, this is very strange. If there is some other location for 
the files and EMBOSS_* environment variables are being used to redirect 
that would explain the behaviour.

What is the message you get from Jemboss?

> The emboss doc at
http://emboss.sourceforge.net/docs/adminguide/node69.html
> says:
>>> Graphical interfaces to EMBOSS
> This chapter needs to be written. It will be written when the
available GUIs
> are stable enough to document.
> <<
> 
> Does this mean that Jemboss is not to be trusted? Is not ready for
> prime-time? 

Jemboss is fine. We are updating all our documentation at the moment :-)

> Does anyone know what where and what resource file Jemboss must see so
that
> it can run programs like remap successfully?

You will get a more detailed reply from the Jemboss experts.

regards,

Peter