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]" <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > Sent: Thursday, April 24, 2008 3:49 AM > To: Staffa, Nick (NIH/NIEHS) [C] > Cc: [email protected]; 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 > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
