EMBOSS whish list

Guy Bottu gbottu at ben.vub.ac.be
Wed Aug 15 16:11:41 UTC 2001

from : BEN

	Dear colleagues,
I know it is easy to say "we need this, we need that !", while it takes so much 
time and effort to program. Nevertheless, I take the liberty to make a few 
suggestions for improvements that would help EMBOSS to equal and even surpass 
GCG in userfriendliness :

- for graphic display : an X-Window graphic with "zoom" function, also tektronix 
emulation in color.
- a mechanism to easily submit programs to a "batch queue" from the command line 
(comparable to the -batch parameter of GCG and egcg)
- at the present it is difficult to find out which data file(s) a program uses 
and hence to put an alternative data file in the working directory. You have to 
read exhaustively the on-line manual. It would be nice if there was always a 
command line parameter with default value that would appear if you do
xxx -help
or alternatively maybe a new General Parameter to make
e.g.   xxx -datafile
to make a program display its data file names. The data file name should 
preferable appear in the ACD file so that the parsers that generate pages for 
the graphical user interfaces can find it.
- the possibility to input/output sequences from any program in any format 
should be extended to other kinds of data. E.g.
  base/aa symbol comparison tables : GCG, BLAST, SIM,...
  codon usage tables : GCG, CUTG,...
  3D structures : PDB, Kinemage,...   (is already being done ?)

	Guy Bottu 

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