The glimmer3 package has a bunch of binaries and 3 shell scripts. The "extract" app is called by all the shell scripts, but it does not necessarily have to be in $PATH. Here are the relevant lines from the shell scrips:

/usr/local/bin/g3-from-scratch.csh:$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
/usr/local/bin/g3-from-scratch.csh:  echo "Failed to extract training sequences"
/usr/local/bin/g3-from-training.csh:  echo "in file <coords> to extract a training set.  Use <tag> to prefix"
/usr/local/bin/g3-from-training.csh:$glimmerpath/extract -t $genome $coords > $tag.train
/usr/local/bin/g3-from-training.csh:  echo "Failed to extract training sequences"
/usr/local/bin/g3-from-training.csh:   | $glimmerpath/extract $genome - > $tag.upstream
/usr/local/bin/g3-iterated.csh:$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
/usr/local/bin/g3-iterated.csh:  echo "Failed to extract training sequences"
/usr/local/bin/g3-iterated.csh:   | $glimmerpath/extract $genome - > $tag.upstream

All the apps, including glimmer3 itself, are expected to be in $glimmerpath, e.g.:

/usr/local/bin/g3-from-training.csh:$glimmerpath/glimmer3 $glimmeropts -b $tag.motif -P $startuse $genome $tag.icm $tag

Personally I never use the apps directly, I always use the shell scripts. Should we put all the apps in lib and set $glimmerpath to the lib location?



On Jan 12, 2013, at 3:20 AM, Samuel John <notifications@github.com> wrote:

> In glimmer302a.rb:
> 
> > +require 'tmpdir'
> > +
> > +class Glimmer302a < Formula
> > +  homepage 'http://www.cbcb.umd.edu/software/glimmer/'
> > +  url 'http://www.cbcb.umd.edu/software/glimmer/glimmer302a.tar.gz'
> > +  sha1 '27fbd2498f997e0a47026b348b2fc95b073b712a'
> > +  version '3.02'
> > +
> > +  def install
> > +    cd 'src' do
> > +      system 'make'
> > +    end
> > +
> > +    cd 'bin' do
> > +      bin.install %w[window-acgt start-codon-distrib long-orfs entropy-score build-fixed uncovered
> > +       score-fixed glimmer3 entropy-profile anomaly multi-extract extract build-icm]
> Are all these binaries needed, or do you just call one main binary and the others are internally called? I am asking because "extract" may perhaps be a fairly common name and may conflict when it is symlinked into $(brew --prefix)/bin.
> 
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