Binary-only install of SHRiMP

shrimp.rb

require 'formula'

class Shrimp < Formula
  homepage 'http://compbio.cs.toronto.edu/shrimp/'
  url 'http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_2.macosx.x86_64.tar.gz'
  sha1 'ba666ccc0aa5da0f55a8a41e6f40daabe876c3dd'
  version '2.2.2'

  def patches
    # Change shebang of Python utilities.
    DATA
  end

  def install
    rm "bin/README"
    bin.install Dir["bin/*"]
    cd "utils" do
      rm "README"
      rm Dir["*.c"]
      rm Dir["*.awk"]
      man1.install %w[EXTRACT-SUBSEQUENCE INDEXES MAPPINGS-TOP-HITS MERGE-HITS PROJECT-DB SPLIT-DB SPLIT-PROJECT-DB TESTING]
      chmod 0755, Dir["*.py"]
    end

    libexec.install "utils"
    bin.install_symlink Dir["#{libexec}/utils/*"] - ["#{libexec}/utils/utils.py"]
  end

  def caveats; <<-EOS.undent
    Some utilities will look for the SHRIMP_FOLDER environment variable:
        export SHRIMP_FOLDER=#{libexec}
    EOS
  end
end
__END__
diff --git a/utils/colourise.py b/utils/colourise.py
index 5c0a163..09227af
--- a/utils/colourise.py
+++ b/utils/colourise.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: colourise.py,v 1.2 2008/06/06 18:24:28 rumble Exp $
 
 import sys
diff --git a/utils/cs2ls.py b/utils/cs2ls.py
index a892e33..fa17f17
--- a/utils/cs2ls.py
+++ b/utils/cs2ls.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: cs2ls.py,v 1.1 2008/11/18 20:22:32 rumble Exp $
 
 import sys
diff --git a/utils/extract-subsequence.py b/utils/extract-subsequence.py
index 5f84ffd..74d85d4 100755
--- a/utils/extract-subsequence.py
+++ b/utils/extract-subsequence.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import getopt
 
 import sys
diff --git a/utils/extractseq.py b/utils/extractseq.py
index a3da1ed..1e47fbb
--- a/utils/extractseq.py
+++ b/utils/extractseq.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: extractseq.py,v 1.2 2008/06/06 18:24:28 rumble Exp $
 
 import sys
diff --git a/utils/extractunmapped.py b/utils/extractunmapped.py
index 8afb2bf..f41b8d2
--- a/utils/extractunmapped.py
+++ b/utils/extractunmapped.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: extractunmapped.py,v 1.1 2009/05/15 18:51:03 rumble Exp $
 
 import sys
diff --git a/utils/findpairs.py b/utils/findpairs.py
index 1d7b5d9..f584455 100755
--- a/utils/findpairs.py
+++ b/utils/findpairs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import sys
 
 if len(sys.argv) < 6:
diff --git a/utils/findseq.py b/utils/findseq.py
index 2011a45..7ecbb52
--- a/utils/findseq.py
+++ b/utils/findseq.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: findseq.py,v 1.2 2008/06/06 18:24:28 rumble Exp $
 
 import sys
diff --git a/utils/get_clipped_mappings.py b/utils/get_clipped_mappings.py
index 9e38631..7392f04
--- a/utils/get_clipped_mappings.py
+++ b/utils/get_clipped_mappings.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import sys
 
 def usage():
diff --git a/utils/get_contigs.py b/utils/get_contigs.py
index 7f790d4..b2e5942
--- a/utils/get_contigs.py
+++ b/utils/get_contigs.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import sys, re
 
 
diff --git a/utils/mappings-top-hits.py b/utils/mappings-top-hits.py
index a877ae2..8290469 100755
--- a/utils/mappings-top-hits.py
+++ b/utils/mappings-top-hits.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import os
 import getopt
 import sys
diff --git a/utils/merge-hits-diff-qr-same-db.py b/utils/merge-hits-diff-qr-same-db.py
index e1f62b9..7b3e731 100755
--- a/utils/merge-hits-diff-qr-same-db.py
+++ b/utils/merge-hits-diff-qr-same-db.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import sys
 
 if len(sys.argv) < 3:
diff --git a/utils/mergepairfiles.py b/utils/mergepairfiles.py
index 1968a16..a1456d5
--- a/utils/mergepairfiles.py
+++ b/utils/mergepairfiles.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import sys
 
 if len(sys.argv) < 3:
diff --git a/utils/project-db.py b/utils/project-db.py
index 88c36e6..f935f18 100755
--- a/utils/project-db.py
+++ b/utils/project-db.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import subprocess
 import sys
 import os
diff --git a/utils/revcmpl.py b/utils/revcmpl.py
old mode 100644
new mode 100755
index 386b183..f6bdae8
--- a/utils/revcmpl.py
+++ b/utils/revcmpl.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: revcmpl.py,v 1.2 2008/06/06 18:24:28 rumble Exp $
 
 import sys
diff --git a/utils/split-db.py b/utils/split-db.py
index 968bc99..d5804ca 100755
--- a/utils/split-db.py
+++ b/utils/split-db.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import subprocess
 import sys
 import os
diff --git a/utils/split-project-db.py b/utils/split-project-db.py
index 4c5401e..3d7f1c4 100755
--- a/utils/split-project-db.py
+++ b/utils/split-project-db.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import subprocess
 import sys
 import os
diff --git a/utils/splitreads.py b/utils/splitreads.py
index bf27d80..928d617
--- a/utils/splitreads.py
+++ b/utils/splitreads.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 #	$Id: splitreads.py,v 1.3 2009/03/06 18:58:49 rumble Exp $
 
 import sys
diff --git a/utils/splittigs.py b/utils/splittigs.py
index 46c26ac..ac4cacc
--- a/utils/splittigs.py
+++ b/utils/splittigs.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #	$Id: splittigs.py,v 1.2 2008/06/06 18:24:28 rumble Exp $
 
 import sys