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;