[BioRuby] How to install EMBOSS suites in my local environment?

[Toshiaki Katayama]

On 2008/01/10, at 6:24, Sharvari Gujja wrote:
> when I use the exec command in bioruby1.2.1 , i get the following error:
>
> C:/Program Files/ruby/lib/ruby/site_ruby/1.8/bio/appl/emboss.rb:135:in `exec': undefined method `close' for nil:NilClass (NoMethodError)
>   from Z:/emboss1.rb:11

I suspect that the EMBOSS command couldn't be found.
Firstly, please confirm you can run the command in the terminal.
Secondary, check the command search path.

> transeq -sbegin 110 -send 1171 embl:xlrhodop

Then,

On 2008/01/10, at 8:12, Sharvari Gujja wrote:
> How can I use fasta files from NCBI as input to asequence and bsequence?
>
> For examples , I have 2 fasta files BA000002.fasta and CP000030.fasta

learn EMBOSS USA (Uniform Sequence Address) at

http://emboss.sourceforge.net/docs/
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html

Toshiaki