diff options
| author | Felix Golatofski | 2020-02-09 20:18:50 +0100 |
|---|---|---|
| committer | Felix Golatofski | 2020-02-09 20:18:50 +0100 |
| commit | 7e24ef6e105fb3ca0e2f01a33a18dfa38d1102af (patch) | |
| tree | 7a21a7628ee8c7a37a801f2fb394ad0b89082d71 | |
| parent | 323c015df150e455a62e3c262f979b1034e4457b (diff) | |
| download | aur-7e24ef6e105fb3ca0e2f01a33a18dfa38d1102af.tar.gz | |
Updated to 4.8.1
| -rw-r--r-- | .SRCINFO | 10 | ||||
| -rw-r--r-- | PKGBUILD | 8 | ||||
| -rw-r--r-- | perl-shebangs.patch | 433 |
3 files changed, 441 insertions, 10 deletions
@@ -1,18 +1,16 @@ -# Generated by mksrcinfo v8 -# Sun Mar 6 22:20:56 UTC 2016 pkgbase = cd-hit pkgdesc = clustering DNA/protein sequence database at high identity with tolerance - pkgver = 4.6.5 + pkgver = 4.8.1 pkgrel = 1 url = http://weizhongli-lab.org/cd-hit/ arch = i686 arch = x86_64 license = GPL2 depends = perl - source = https://github.com/weizhongli/cdhit/releases/download/V4.6.5/cd-hit-v4.6.5-2016-0304.tar.gz + source = https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz source = perl-shebangs.patch::https://patch-diff.githubusercontent.com/raw/weizhongli/cdhit/pull/25.patch - md5sums = fabe71cabf963591cf6e0b9458f88f7f - md5sums = 921ad2a919b3be7a9d3a629f98469b72 + sha512sums = e01247d20c7f4035ea775e4b27a4ab1d34acdcce17cf01c2fe08a2478220655266c2a25149cecb9aa987d2b43bd6530e2e846b2781c373d12fd493fc89a575e6 + sha512sums = f9a918ebe2865d84c31fbd5ab4b0b2f58bf3faee879cb304e1fa44969e01db3786f12b3699a712094f9ee261efd306188aff548b1a88f57daae5d02205551236 pkgname = cd-hit @@ -1,8 +1,8 @@ # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> pkgname=cd-hit -pkgver=4.6.5 -_pkgver="v$pkgver-2016-0304" +pkgver=4.8.1 +_pkgver="v$pkgver-2019-0228" pkgrel=1 pkgdesc="clustering DNA/protein sequence database at high identity with tolerance" arch=('i686' 'x86_64') @@ -11,8 +11,8 @@ license=('GPL2') depends=('perl') source=("https://github.com/weizhongli/cdhit/releases/download/V$pkgver/cd-hit-$_pkgver.tar.gz" "perl-shebangs.patch::https://patch-diff.githubusercontent.com/raw/weizhongli/cdhit/pull/25.patch") -md5sums=('fabe71cabf963591cf6e0b9458f88f7f' - '921ad2a919b3be7a9d3a629f98469b72') +sha512sums=('e01247d20c7f4035ea775e4b27a4ab1d34acdcce17cf01c2fe08a2478220655266c2a25149cecb9aa987d2b43bd6530e2e846b2781c373d12fd493fc89a575e6' + 'f9a918ebe2865d84c31fbd5ab4b0b2f58bf3faee879cb304e1fa44969e01db3786f12b3699a712094f9ee261efd306188aff548b1a88f57daae5d02205551236') prepare() { cd $srcdir/cd-hit-$_pkgver diff --git a/perl-shebangs.patch b/perl-shebangs.patch new file mode 100644 index 000000000000..088b513556a5 --- /dev/null +++ b/perl-shebangs.patch @@ -0,0 +1,433 @@ +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; + $script_dir =~ s/[^\/]+$//; |