Updated to 4.8.1

1 files changed, 0 insertions, 433 deletions

diff --git a/perl-shebangs.patch b/perl-shebangs.patch
deleted file mode 100644
index 088b513556a5..000000000000
--- a/perl-shebangs.patch
+++ /dev/null
@@ -1,433 +0,0 @@
-From eae2a63c25fcb95e6fc1e6e062215ad1e8b24345 Mon Sep 17 00:00:00 2001
-From: Christian Krause <kizkizzbangbang@googlemail.com>
-Date: Thu, 16 Jul 2015 12:33:10 +0200
-Subject: [PATCH] use more portable /usr/bin/env perl for scripts
-
-This is useful, e.g. if your perl is not installed in /usr/bin or you
-want to give a specific perl precendence over the one installed in
-/usr/bin. Wherever there was `perl -w` there is now `use warnings;`.
----
- cd-hit-2d-para.pl                     | 3 ++-
- cd-hit-auxtools/cd-hit-dup-PE-out.pl  | 2 +-
- cd-hit-div.pl                         | 2 +-
- cd-hit-para.pl                        | 3 ++-
- clstr2tree.pl                         | 2 +-
- clstr2txt.pl                          | 2 +-
- clstr2xml.pl                          | 2 +-
- clstr_cut.pl                          | 2 +-
- clstr_merge.pl                        | 2 +-
- clstr_merge_noorder.pl                | 2 +-
- clstr_quality_eval.pl                 | 2 +-
- clstr_quality_eval_by_link.pl         | 2 +-
- clstr_reduce.pl                       | 2 +-
- clstr_renumber.pl                     | 2 +-
- clstr_rep.pl                          | 2 +-
- clstr_reps_faa_rev.pl                 | 2 +-
- clstr_rev.pl                          | 2 +-
- clstr_select.pl                       | 2 +-
- clstr_select_rep.pl                   | 2 +-
- clstr_size_histogram.pl               | 2 +-
- clstr_size_stat.pl                    | 2 +-
- clstr_sort_by.pl                      | 2 +-
- clstr_sort_prot_by.pl                 | 2 +-
- clstr_sql_tbl.pl                      | 2 +-
- clstr_sql_tbl_sort.pl                 | 2 +-
- make_multi_seq.pl                     | 2 +-
- plot_2d.pl                            | 2 +-
- plot_len1.pl                          | 2 +-
- psi-cd-hit/cd-hit-div.pl              | 2 +-
- psi-cd-hit/clstr_select_rep.pl        | 2 +-
- psi-cd-hit/clstr_select_seq.pl        | 2 +-
- psi-cd-hit/fetch_fasta_by_ids.pl      | 2 +-
- psi-cd-hit/fetch_fasta_exclude_ids.pl | 2 +-
- psi-cd-hit/psi-2d.pl                  | 2 +-
- psi-cd-hit/psi-cd-hit-local.pl        | 3 ++-
- psi-cd-hit/psi-cd-hit.pl              | 4 +++-
- 36 files changed, 41 insertions(+), 36 deletions(-)
-
-diff --git a/cd-hit-2d-para.pl b/cd-hit-2d-para.pl
-index 3cab955..9aa2d8a 100755
---- 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/
-@@ -11,6 +11,7 @@
- #                                      Email liwz@sdsc.edu
- # =============================================================================
- 
-+use warnings;
- use strict;
- no strict "refs";
- 
-diff --git a/cd-hit-auxtools/cd-hit-dup-PE-out.pl b/cd-hit-auxtools/cd-hit-dup-PE-out.pl
-index bfe5af3..f035229 100755
---- a/cd-hit-auxtools/cd-hit-dup-PE-out.pl
-+++ b/cd-hit-auxtools/cd-hit-dup-PE-out.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $script_name = $0;
- my $script_dir = $0;
-diff --git a/cd-hit-div.pl b/cd-hit-div.pl
-index e349394..db8d942 100755
---- 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
-diff --git a/cd-hit-para.pl b/cd-hit-para.pl
-index 33f1a1b..db62e38 100755
---- 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/
-@@ -11,6 +11,7 @@
- #                                      Email liwz@sdsc.edu
- # =============================================================================
- 
-+use warnings;
- use strict;
- no strict "refs";
- 
-diff --git a/clstr2tree.pl b/clstr2tree.pl
-index 73fd37a..56d9fe2 100755
---- 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
-diff --git a/clstr2txt.pl b/clstr2txt.pl
-index 902b083..127537e 100755
---- a/clstr2txt.pl
-+++ b/clstr2txt.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $no = 0;
- my $clstr_no = "";
-diff --git a/clstr2xml.pl b/clstr2xml.pl
-index 10d828c..ba8264a 100755
---- 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
-diff --git a/clstr_cut.pl b/clstr_cut.pl
-index 498f180..ae0264c 100755
---- a/clstr_cut.pl
-+++ b/clstr_cut.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #keep only top $no proteins in cluster
- 
-diff --git a/clstr_merge.pl b/clstr_merge.pl
-index 3fe108e..9186777 100755
---- a/clstr_merge.pl
-+++ b/clstr_merge.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- # the order of clusters need to be identical
- my ($master_clstr, @clstr) = @ARGV;
-diff --git a/clstr_merge_noorder.pl b/clstr_merge_noorder.pl
-index f8acdfc..0852aee 100755
---- 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
-diff --git a/clstr_quality_eval.pl b/clstr_quality_eval.pl
-index 62f2a3d..060ab01 100755
---- 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
-diff --git a/clstr_quality_eval_by_link.pl b/clstr_quality_eval_by_link.pl
-index 8fba8df..140c05c 100755
---- 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
-diff --git a/clstr_reduce.pl b/clstr_reduce.pl
-index 990f4ad..3621025 100755
---- a/clstr_reduce.pl
-+++ b/clstr_reduce.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- 
- $file90 = shift;
-diff --git a/clstr_renumber.pl b/clstr_renumber.pl
-index b542304..c66088d 100755
---- 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+)/) {
-diff --git a/clstr_rep.pl b/clstr_rep.pl
-index 0ebeb88..84b86b3 100755
---- a/clstr_rep.pl
-+++ b/clstr_rep.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- $rep = "";
- $no = 0;
-diff --git a/clstr_reps_faa_rev.pl b/clstr_reps_faa_rev.pl
-index 80a4a8a..3574b2b 100755
---- 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
- 
-diff --git a/clstr_rev.pl b/clstr_rev.pl
-index d7efdcc..71134e2 100755
---- 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
-diff --git a/clstr_select.pl b/clstr_select.pl
-index 1b168d9..dc70147 100755
---- a/clstr_select.pl
-+++ b/clstr_select.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #my $by = shift;
- my $min;
-diff --git a/clstr_select_rep.pl b/clstr_select_rep.pl
-index 80c7b7e..f7c38f4 100755
---- 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;
-diff --git a/clstr_size_histogram.pl b/clstr_size_histogram.pl
-index 01ecb63..b726e46 100755
---- 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";
-diff --git a/clstr_size_stat.pl b/clstr_size_stat.pl
-index b234b06..ecda7db 100755
---- 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";
-diff --git a/clstr_sort_by.pl b/clstr_sort_by.pl
-index 82e9cf8..adb12d8 100755
---- 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;
-diff --git a/clstr_sort_prot_by.pl b/clstr_sort_prot_by.pl
-index 64f19e2..0832b99 100755
---- 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);
-diff --git a/clstr_sql_tbl.pl b/clstr_sql_tbl.pl
-index f2dba07..68bfd7d 100755
---- 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";
-diff --git a/clstr_sql_tbl_sort.pl b/clstr_sql_tbl_sort.pl
-index 67d60a8..3dfe9c4 100755
---- 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";
-diff --git a/make_multi_seq.pl b/make_multi_seq.pl
-index 7b05636..3678654 100755
---- 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
-diff --git a/plot_2d.pl b/plot_2d.pl
-index 418a5cf..91342ca 100755
---- a/plot_2d.pl
-+++ b/plot_2d.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- use Image::Magick;
- 
-diff --git a/plot_len1.pl b/plot_len1.pl
-index efcdfe0..e8be6e3 100755
---- a/plot_len1.pl
-+++ b/plot_len1.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- $file90 = shift;
- $segs = shift;
-diff --git a/psi-cd-hit/cd-hit-div.pl b/psi-cd-hit/cd-hit-div.pl
-index e349394..db8d942 100755
---- a/psi-cd-hit/cd-hit-div.pl
-+++ b/psi-cd-hit/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
-diff --git a/psi-cd-hit/clstr_select_rep.pl b/psi-cd-hit/clstr_select_rep.pl
-index b465586..63db0ce 100755
---- a/psi-cd-hit/clstr_select_rep.pl
-+++ b/psi-cd-hit/clstr_select_rep.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $by = shift;
- my $min;
-diff --git a/psi-cd-hit/clstr_select_seq.pl b/psi-cd-hit/clstr_select_seq.pl
-index fd7bb8b..598b0e9 100755
---- a/psi-cd-hit/clstr_select_seq.pl
-+++ b/psi-cd-hit/clstr_select_seq.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $by = shift;
- my $min;
-diff --git a/psi-cd-hit/fetch_fasta_by_ids.pl b/psi-cd-hit/fetch_fasta_by_ids.pl
-index bfdbb26..9c17504 100755
---- a/psi-cd-hit/fetch_fasta_by_ids.pl
-+++ b/psi-cd-hit/fetch_fasta_by_ids.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my ($gi_file, $seq_file) = @ARGV;
- 
-diff --git a/psi-cd-hit/fetch_fasta_exclude_ids.pl b/psi-cd-hit/fetch_fasta_exclude_ids.pl
-index 90e237e..13d061a 100755
---- a/psi-cd-hit/fetch_fasta_exclude_ids.pl
-+++ b/psi-cd-hit/fetch_fasta_exclude_ids.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my ($gi_file, $seq_file) = @ARGV;
- 
-diff --git a/psi-cd-hit/psi-2d.pl b/psi-cd-hit/psi-2d.pl
-index ab3f655..f3884a3 100755
---- a/psi-cd-hit/psi-2d.pl
-+++ b/psi-cd-hit/psi-2d.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- 
- my $script_name = $0;
-diff --git a/psi-cd-hit/psi-cd-hit-local.pl b/psi-cd-hit/psi-cd-hit-local.pl
-index a77c7f7..e7866c3 100755
---- a/psi-cd-hit/psi-cd-hit-local.pl
-+++ b/psi-cd-hit/psi-cd-hit-local.pl
-@@ -1,7 +1,8 @@
--#!/usr/bin/perl -w
-+#!/usr/bin/env perl
- ################################################################################
- ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
- ################################################################################
-+use warnings;
- our $pid       = $$;
- our $db_in     = "";   ###################
- our $db_out    = "";   # input / output
-diff --git a/psi-cd-hit/psi-cd-hit.pl b/psi-cd-hit/psi-cd-hit.pl
-index af99e52..35aaeda 100755
---- a/psi-cd-hit/psi-cd-hit.pl
-+++ b/psi-cd-hit/psi-cd-hit.pl
-@@ -1,8 +1,10 @@
--#!/usr/bin/perl -w
-+#!/usr/bin/env perl
- ################################################################################
- ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
- ################################################################################
- 
-+use warnings;
-+
- our $script_name = $0;
- our $script_dir = $0;
-    $script_dir =~ s/[^\/]+$//;