[EMBOSS] Jemboss

[Staffa, Nick (NIH/NIEHS)]

You have hit the nail on the head.
(probably) 
or to quote Jeeves:
"Rem acu tetigisti."


On 4/24/08 11:48 AM, "Tim Carver" <tjc at sanger.ac.uk> wrote:

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