gentoo-overlay/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch

Make perl shebangs more Prefix friendly
See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/

--- a/cd-hit-2d-para.pl
+++ b/cd-hit-2d-para.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 # =============================================================================
 # CD-HIT
 # http://cd-hit.org/
--- a/cd-hit-div.pl
+++ b/cd-hit-div.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #not like cd-hit-div, this script do not sort input
 #or throw away seq
--- a/cd-hit-para.pl
+++ b/cd-hit-para.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 # =============================================================================
 # CD-HIT
 # http://cd-hit.org/
--- a/clstr2tree.pl
+++ b/clstr2tree.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $clstr = shift;
 $fr = shift; # for nr80.clstr $fr = 0.8
--- a/clstr2txt.pl
+++ b/clstr2txt.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $no = 0;
 my $clstr_no = "";
--- a/clstr2xml.pl
+++ b/clstr2xml.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...]
 #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results
--- a/clstr_cut.pl
+++ b/clstr_cut.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #keep only top $no proteins in cluster
 
--- a/clstr_merge_noorder.pl
+++ b/clstr_merge_noorder.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # order of clusters don't need to be the same
 # but then I have to read everything into memory
--- a/clstr_merge.pl
+++ b/clstr_merge.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # the order of clusters need to be identical
 my ($master_clstr, @clstr) = @ARGV;
--- a/clstr_quality_eval_by_link.pl
+++ b/clstr_quality_eval_by_link.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ## calculate the sensitivity and specificity of clusters
 ## if the input fasta file has pre-defined classification term
--- a/clstr_quality_eval.pl
+++ b/clstr_quality_eval.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ## calculate the sensitivity and specificity of clusters
 ## if the input fasta file has pre-defined classification term
--- a/clstr_reduce.pl
+++ b/clstr_reduce.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 
 $file90 = shift;
--- a/clstr_renumber.pl
+++ b/clstr_renumber.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 $no = 0;
 while($ll=<>){
   if ($ll =~ /^>Cluster (\d+)/) {
--- a/clstr_rep.pl
+++ b/clstr_rep.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $rep = "";
 $no = 0;
--- a/clstr_reps_faa_rev.pl
+++ b/clstr_reps_faa_rev.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # output single fasta file
 # for each cluster output at least $cutoff seqs
 
--- a/clstr_rev.pl
+++ b/clstr_rev.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # if nr90 from nr100 and
 #    nr80 from nr90, so I have nr90.clstr and nr80.clstr
 # but, in nr80.clstr, some gi numbers whose from nr100 are there
--- a/clstr_select.pl
+++ b/clstr_select.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #my $by = shift;
 my $min;
--- a/clstr_select_rep.pl
+++ b/clstr_select_rep.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #my $by = shift;
 my $min;
--- a/clstr_size_histogram.pl
+++ b/clstr_size_histogram.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n";
--- a/clstr_size_stat.pl
+++ b/clstr_size_stat.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_size_stat.pl clstr_file\n";
--- a/clstr_sort_by.pl
+++ b/clstr_sort_by.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $sort_by_what = shift;
    $sort_by_what = "no" unless $sort_by_what;
--- a/clstr_sort_prot_by.pl
+++ b/clstr_sort_prot_by.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $sort_by = shift;
    $sort_by = "len" unless ($sort_by);
--- a/clstr_sql_tbl.pl
+++ b/clstr_sql_tbl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
   print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n";
--- a/clstr_sql_tbl_sort.pl
+++ b/clstr_sql_tbl_sort.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n";
--- a/make_multi_seq.pl
+++ b/make_multi_seq.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #note you have to use "-d 0" in the cd-hit run
 #note you better to use "-g 1" in the cd-hit run
--- a/plot_2d.pl
+++ b/plot_2d.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Image::Magick;
 
--- a/plot_len1.pl
+++ b/plot_len1.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $file90 = shift;
 $segs = shift;