sci-biology/cd-hit: Version bump to 4.6.6

Package-Manager: Portage-2.3.3, Repoman-2.3.1

2 files changed, 341 insertions, 0 deletions

diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch
new file mode 100644
index 000000000000..c668d5c6154e
--- /dev/null
+++ b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch
@@ -0,0 +1,122 @@
+Fix build system, in order to honour user variables
+
+--- a/makefile
++++ b/makefile
+@@ -1,7 +1,4 @@
+-
+-CC = g++ -Wall -ggdb
+-CC = g++ -pg
+-CC = g++
++CXX ?= g++
+ 
+ # without OpenMP
+ 
+@@ -9,35 +6,19 @@
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),no)
+-  CCFLAGS = -DNO_OPENMP
+-else
+-  CCFLAGS = -fopenmp
+-endif
+-
+-# support debugging
+-# in command line:
+-# make debug=yes
+-# make openmp=yes debug=yes
+-ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++  my_CPPFLAGS = -DNO_OPENMP
+ else
+-CCFLAGS += -O2
++  my_CXXFLAGS = -fopenmp
+ endif
+ 
+ ifdef MAX_SEQ
+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
++my_CPPFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+ endif
+ 
+-#LDFLAGS = -static -o
+-LDFLAGS += -o
+-
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+ 
+-# Propagate hardening flags
+-CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
+-
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -47,52 +28,52 @@
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
+ 
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-div.c++ -c
+ 
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
++	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-454.c++ -c
+ 
+ PREFIX ?= /usr/local/bin
+ 
+ install:
+ 	for prog in $(PROGS); do \
+-		install -m 0755 $$prog $(PREFIX); \
++		install -m 0755 $$prog $(DESTDIR)$(PREFIX); \
+ 	done
+-	install -m 0755 *.pl $(PREFIX);
++	install -m 0755 *.pl $(DESTDIR)$(PREFIX);
diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch
new file mode 100644
index 000000000000..3784296f2e94
--- /dev/null
+++ b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch
@@ -0,0 +1,219 @@
+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;