[EMBOSS] Jemboss

[Tim Carver]

Hi Nick

I would check 'jemboss.properties' to ensure that embossData is set to the
correct directory. See the description at:

http://emboss.sourceforge.net/Jemboss/install/properties.html

Regards
Tim

On 24/4/08 16:02, "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov>
wrote:

> 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
> 
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