gentoo-overlay/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch

* Fix ancient perl 4 modules that are long gone.
* Fix perl shebangs to be portable and usable on Prefix.
See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/

--- a/squid/Testsuite/bug-1-sfetch-paths
+++ b/squid/Testsuite/bug-1-sfetch-paths
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 # Test for bug #1: sfetch/SSI path bug.
 # sfetch can't follow paths out of current directory if it's using
--- a/squid/Testsuite/x-base-afetch
+++ b/squid/Testsuite/x-base-afetch
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/squid/Testsuite/x-base-alistat
+++ b/squid/Testsuite/x-base-alistat
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/squid/Testsuite/x-base-seqstat
+++ b/squid/Testsuite/x-base-seqstat
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/squid/Testsuite/x-base-sfetch
+++ b/squid/Testsuite/x-base-sfetch
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/squid/Testsuite/x-base-shuffle
+++ b/squid/Testsuite/x-base-shuffle
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/squid/Testsuite/x-base-sindex
+++ b/squid/Testsuite/x-base-sindex
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/squid/Testsuite/x-base-sreformat
+++ b/squid/Testsuite/x-base-sreformat
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 use testsuite;
 
--- a/testsuite/sqc
+++ b/testsuite/sqc
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 # sqc 
 # quality control script for exercising code, regression testing, 
@@ -176,12 +176,11 @@
 # SRE, Tue Aug  6 11:16:39 2002
 # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $
 
-require "getopts.pl";
-require "importenv.pl";
+use Getopt::Std;
 
 # Parse our command line
 #
-&Getopts('mp:r:v');
+getopts('mp:r:v');
 if ($opt_m) { $do_memtest = 1;    }
 if ($opt_p) { push @prepdirs, $opt_p; }
 if ($opt_r) { push @olddirs,  $opt_r; }
@@ -506,7 +505,7 @@
 #
 sub tempname {
     my ($dir, $name, $suffix);
-    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
+    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
 
     foreach $suffix ("aa".."zz") {
         $name = "$dir"."sre".$suffix.$$;
--- a/testsuite/test1-conversion.pl
+++ b/testsuite/test1-conversion.pl
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 
 # Test hmmconvert.
 #