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* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cd-hit/files/, sci-biology/cd-hit/
@ 2017-02-25 19:19 David Seifert
  0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-02-25 19:19 UTC (permalink / raw
  To: gentoo-commits

commit:     348f9c5b9150fcbc7aac389c76e9ed702395c066
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 19:15:53 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 19:18:32 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=348f9c5b

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

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/cd-hit/Manifest                        |   1 +
 sci-biology/cd-hit/cd-hit-4.6.6.ebuild             |  48 +++++
 .../files/cd-hit-4.6.6-fix-build-system.patch      | 122 ++++++++++++
 .../files/cd-hit-4.6.6-fix-perl-shebangs.patch     | 219 +++++++++++++++++++++
 4 files changed, 390 insertions(+)

diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
index 5d2ddfeed2..b671c47b32 100644
--- a/sci-biology/cd-hit/Manifest
+++ b/sci-biology/cd-hit/Manifest
@@ -1,3 +1,4 @@
+DIST cd-hit-4.6.6.tar.gz 1152570 SHA256 97946f8ae62c3efa20ad4c527b8ea22200cf1b75c9941fb14de2bdaf1d6910f1 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 WHIRLPOOL 4ee404e34a9c22aef0b809568aa1a7cefcd8d08e4a8c97d1c65b7692ae14b0567e5cc446054083219b56e89895117f69f786e6183f6c67d03d1f8404f7ba9632
 DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 SHA512 84beba384eb6e9bcf94c7e2ca63f862493fc0d058ad186752524a09016e01274229ca9b7a5275cd5454f54488235a6949e17090ffbf68ff441a613dbe5cf05a8 WHIRLPOOL 698d72f347b92091ade411bdbf540f4b4eeea6c742d3766e891bede7f1aa03024bd2f611a4235a6dec0ed9b9b5e06b3d69a7b8e6a7ab7d8139297b5a8b0da9d2
 DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a SHA512 a093d15e26d6e226e5b37e43ed36affe58c0ee265bd43fd2098a39eafb54c7154ee1a7585da785324dc57532abe3401d48ad5a4a2de080fa6e1422091083683a WHIRLPOOL 3e2ea2db07ecc553d5f03f13a1092e85211257fb4a681629be0350d9cc3f3cc384d24bdb8b3e31d3f469fbc93070363afee608904b9ce3956ca24a8fa6d4d8e5
 DIST cd-hit-v4.6-2012-04-25.tgz 652228 SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9 SHA512 1004a4190643b6f5f1da067a4b911abc068d0bf7d909edd84f45d5fe9a1b17eb3276c0ddde391cbc5053a9ab979d09cbbe832615b7cce4fc2aeefce1d1bec52c WHIRLPOOL 1c7a50e40e9753c035a2920af09b024e9403f4a7cf1a801b998afd5b64189256857a236439f5b2935603fd4a691a722a9d74c3a373ab66c79faee9d8335834b4

diff --git a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.6.ebuild
new file mode 100644
index 0000000000..49bea96899
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.6.6.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+RELDATE="2016-0711"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="https://github.com/weizhongli/cdhit/releases/download/V${PV}/${RELEASE}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="openmp"
+
+RDEPEND="dev-lang/perl"
+
+S="${WORKDIR}"/${RELEASE}
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.6.6-fix-perl-shebangs.patch
+	"${FILESDIR}"/${PN}-4.6.6-fix-build-system.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_compile() {
+	tc-export CXX
+	emake openmp=$(usex openmp)
+}
+
+src_install() {
+	dodir /usr/bin
+	PREFIX="${EPREFIX}"/usr/bin default
+
+	dodoc doc/*.pdf
+}

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 0000000000..c668d5c615
--- /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 0000000000..3784296f2e
--- /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;


^ permalink raw reply related	[flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/cd-hit/files/, sci-biology/cd-hit/
@ 2017-02-25 19:19 David Seifert
  0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-02-25 19:19 UTC (permalink / raw
  To: gentoo-commits

commit:     297c25831be85619015cb3f854b757570601bb5e
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 19:17:42 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 19:18:39 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=297c2583

sci-biology/cd-hit: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/cd-hit/Manifest                 |   3 -
 sci-biology/cd-hit/cd-hit-4.5.1.ebuild      |  42 ----------
 sci-biology/cd-hit/cd-hit-4.5.4.ebuild      |  43 ----------
 sci-biology/cd-hit/cd-hit-4.6.ebuild        |  44 -----------
 sci-biology/cd-hit/files/4.5.1-gentoo.patch |  85 --------------------
 sci-biology/cd-hit/files/4.5.4-gentoo.patch |  98 -----------------------
 sci-biology/cd-hit/files/4.6-gentoo.patch   | 117 ----------------------------
 7 files changed, 432 deletions(-)

diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
index b671c47b32..f2d3e0b6ed 100644
--- a/sci-biology/cd-hit/Manifest
+++ b/sci-biology/cd-hit/Manifest
@@ -1,4 +1 @@
 DIST cd-hit-4.6.6.tar.gz 1152570 SHA256 97946f8ae62c3efa20ad4c527b8ea22200cf1b75c9941fb14de2bdaf1d6910f1 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 WHIRLPOOL 4ee404e34a9c22aef0b809568aa1a7cefcd8d08e4a8c97d1c65b7692ae14b0567e5cc446054083219b56e89895117f69f786e6183f6c67d03d1f8404f7ba9632
-DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 SHA512 84beba384eb6e9bcf94c7e2ca63f862493fc0d058ad186752524a09016e01274229ca9b7a5275cd5454f54488235a6949e17090ffbf68ff441a613dbe5cf05a8 WHIRLPOOL 698d72f347b92091ade411bdbf540f4b4eeea6c742d3766e891bede7f1aa03024bd2f611a4235a6dec0ed9b9b5e06b3d69a7b8e6a7ab7d8139297b5a8b0da9d2
-DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a SHA512 a093d15e26d6e226e5b37e43ed36affe58c0ee265bd43fd2098a39eafb54c7154ee1a7585da785324dc57532abe3401d48ad5a4a2de080fa6e1422091083683a WHIRLPOOL 3e2ea2db07ecc553d5f03f13a1092e85211257fb4a681629be0350d9cc3f3cc384d24bdb8b3e31d3f469fbc93070363afee608904b9ce3956ca24a8fa6d4d8e5
-DIST cd-hit-v4.6-2012-04-25.tgz 652228 SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9 SHA512 1004a4190643b6f5f1da067a4b911abc068d0bf7d909edd84f45d5fe9a1b17eb3276c0ddde391cbc5053a9ab979d09cbbe832615b7cce4fc2aeefce1d1bec52c WHIRLPOOL 1c7a50e40e9753c035a2920af09b024e9403f4a7cf1a801b998afd5b64189256857a236439f5b2935603fd4a691a722a9d74c3a373ab66c79faee9d8335834b4

diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
deleted file mode 100644
index e1eeac9a03..0000000000
--- a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2011-01-31"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://cdhit.googlecode.com/files/${RELEASE}.tgz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE="openmp"
-
-S="${WORKDIR}"/${RELEASE}
-
-pkg_setup() {
-	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare() {
-	tc-export CXX
-	use openmp || append-flags -DNO_OPENMP
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	local myconf=
-	use openmp && myconf="openmp=yes"
-	emake ${myconf} || die
-}
-
-src_install() {
-	dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die
-	dodoc ChangeLog cdhit-user-guide.pdf || die
-}

diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
deleted file mode 100644
index 032aafc43b..0000000000
--- a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2011-03-07"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://cdhit.googlecode.com/files/${RELEASE}.tgz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE="openmp"
-
-S="${WORKDIR}"/${RELEASE}
-
-pkg_setup() {
-	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare() {
-	tc-export CXX
-	use openmp || append-flags -DNO_OPENMP
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	local myconf=
-	use openmp && myconf="openmp=yes"
-	emake ${myconf}
-}
-
-src_install() {
-	dodir /usr/bin
-	emake PREFIX="${ED}/usr/bin" install
-	dodoc ChangeLog cdhit-user-guide.pdf
-}

diff --git a/sci-biology/cd-hit/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild
deleted file mode 100644
index 73c8e48636..0000000000
--- a/sci-biology/cd-hit/cd-hit-4.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2012-04-25"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://cdhit.googlecode.com/files/${RELEASE}.tgz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE="doc openmp"
-
-S="${WORKDIR}"/${RELEASE}
-
-pkg_setup() {
-	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare() {
-	tc-export CXX
-	use openmp || append-flags -DNO_OPENMP
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	local myconf=
-	use openmp && myconf="openmp=yes"
-	emake ${myconf}
-}
-
-src_install() {
-	dodir /usr/bin
-	emake PREFIX="${ED}/usr/bin" install
-	dodoc ChangeLog
-	use doc && dodoc doc/*
-}

diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch
deleted file mode 100644
index c3eaf79cc8..0000000000
--- a/sci-biology/cd-hit/files/4.5.1-gentoo.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-diff --git a/Makefile b/Makefile
-index f1eaa26..92d3130 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
- # in command line: 
- # make openmp=yes
- ifeq ($(openmp),yes)
--CCFLAGS = -O2 -fopenmp
-+CXXFLAGS += -fopenmp
- endif
- 
- # support debugging
-@@ -18,16 +18,16 @@ endif
- # make debug=yes
- # make openmp=yes debug=yes
- ifeq ($(debug),yes)
--CCFLAGS += -ggdb
-+CXXFLAGS += -ggdb
- endif
- 
- #LDFLAGS = -static -o
--LDFLAGS = -o
-+LDFLAGS += -o
- 
- PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div
- 
- .c++.o:
--	$(CC) $(CCFLAGS) -c $<
-+	$(CXX) $(CXXFLAGS) -c $<
- 
- all: $(PROGS)
- 
-@@ -37,39 +37,39 @@ clean:
- # 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) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
- 
- # objects
- cdhit-common.o: cdhit-common.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-common.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
- 
- cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
- 
- cdhit.o: cdhit.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit.c++ -c
- 
- cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
- 
- cdhit-est.o: cdhit-est.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
- 
- cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
- 
- cdhit-div.o: cdhit-div.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-div.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
- 

diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
deleted file mode 100644
index 5aa9b79e02..0000000000
--- a/sci-biology/cd-hit/files/4.5.4-gentoo.patch
+++ /dev/null
@@ -1,98 +0,0 @@
- Makefile |   36 ++++++++++++++++++------------------
- 1 files changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index e8bac1d..bd31093 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
- # in command line: 
- # make openmp=yes
- ifeq ($(openmp),yes)
--CCFLAGS = -O2 -fopenmp
-+CXXFLAGS += -fopenmp
- endif
- 
- # support debugging
-@@ -18,16 +18,16 @@ endif
- # make debug=yes
- # make openmp=yes debug=yes
- ifeq ($(debug),yes)
--CCFLAGS += -ggdb
-+CXXFLAGS += -ggdb
- endif
- 
- #LDFLAGS = -static -o
--LDFLAGS = -o
-+LDFLAGS += -o
- 
- PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
- 
- .c++.o:
--	$(CC) $(CCFLAGS) -c $<
-+	$(CXX) $(CXXFLAGS) -c $<
- 
- all: $(PROGS)
- 
-@@ -37,47 +37,47 @@ clean:
- # 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) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
- 
- # objects
- cdhit-common.o: cdhit-common.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-common.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
- 
- cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
- 
- cdhit.o: cdhit.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit.c++ -c
- 
- cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
- 
- cdhit-est.o: cdhit-est.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
- 
- cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
- 
- cdhit-div.o: cdhit-div.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-div.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
- 
- cdhit-454.o: cdhit-454.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-454.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
- 
- PREFIX ?= /usr/local/bin
- 

diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch
deleted file mode 100644
index 7a376eb8e7..0000000000
--- a/sci-biology/cd-hit/files/4.6-gentoo.patch
+++ /dev/null
@@ -1,117 +0,0 @@
- Makefile |   47 ++++++++++++++++++++++-------------------------
- 1 files changed, 22 insertions(+), 25 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index e9796a1..97dd72b 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,16 +1,13 @@
--
--CC = g++ -Wall -ggdb
--CC = g++ -pg
--CC = g++
-+CXX ?= g++
- 
- # without OpenMP
--CCFLAGS = -DNO_OPENMP
-+#CXXFLAGS = -DNO_OPENMP
- 
- # with OpenMP
- # in command line: 
- # make openmp=yes
- ifeq ($(openmp),yes)
--CCFLAGS = -fopenmp
-+CXXFLAGS += -fopenmp
- endif
- 
- # support debugging
-@@ -18,22 +15,22 @@ endif
- # make debug=yes
- # make openmp=yes debug=yes
- ifeq ($(debug),yes)
--CCFLAGS += -ggdb
-+CXXFLAGS += 
- else
--CCFLAGS += -O2
-+CXXFLAGS += 
- endif
- 
- ifdef MAX_SEQ
--CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
-+CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
- endif
- 
- #LDFLAGS = -static -o
--LDFLAGS = -o
-+#LDFLAGS += -o
- 
- PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
- 
- .c++.o:
--	$(CC) $(CCFLAGS) -c $<
-+	$(CXX) $(CXXFLAGS) -c $<
- 
- all: $(PROGS)
- 
-@@ -43,47 +40,47 @@ clean:
- # 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) $(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) $(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) $(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) $(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) $(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) $(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) $(CXXFLAGS) cdhit-common.c++ -c
- 
- cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
- 
- cdhit.o: cdhit.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit.c++ -c
- 
- cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
- 
- cdhit-est.o: cdhit-est.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
- 
- cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
- 
- cdhit-div.o: cdhit-div.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-div.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
- 
- cdhit-454.o: cdhit-454.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-454.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
- 
- PREFIX ?= /usr/local/bin
- 


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2017-02-25 19:19 David Seifert

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox