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" <[EMAIL PROTECTED]> 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]" <[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 > > > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
