[EMBOSS] to use single program

[Peter Rice]

chowdary manio wrote:

> hello all,
> 
> I am trying to make a tool for alignment using water
> and garnier programs in EMBOSS.
> 
> I want to seperate the code of water and garnier to
> use them alone. I am unable to do that.
> 
> Please let me know a way for this..
> 
> Is it possible to seperate up from EMBOSS?

Water and Garnier link to the EMBOSS libraries. Although you can in theory 
make standalone binaries (the sort yuo can copy to another system and expect 
them to run) it is tricky and we do not officially support EMBOSS programs 
copied that way.

An alternative is to pick up the FASTA package from Virginia. FASTA includes 
the original versions of both garnier and matcher (the other local alignment 
program in EMBOSS - called lalign in FASTA). If you build these programs you 
will be able to copy them. Of course you will lose the EMBOSS standard command 
line checking and output options, but you will find most of the functionality 
you are likely to need is still in the FASTA programs.

Hope that helps,

Peter