cdhit: Testing 4.6.8 release

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 15:11:13 2018 -0500
Changeset:	e46ac3379adc86542d7799d7142f084ef1965fc1

Modified Files:
	Makefile
Added Files:
	cdhit/DESCR
	cdhit/Makefile
	cdhit/PLIST
	cdhit/distinfo

Log Message:
cdhit: Testing 4.6.8 release

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e46ac3379adc86542d7799d7142f084ef1965fc1

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile       |  1 +
 cdhit/DESCR    |  2 ++
 cdhit/Makefile | 44 ++++++++++++++++++++++++++++++++++++++++++++
 cdhit/PLIST    | 38 ++++++++++++++++++++++++++++++++++++++
 cdhit/distinfo |  6 ++++++
 5 files changed, 91 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 52f28f705a..2b5d72c92b 100644
--- a/Makefile
+++ b/Makefile
@@ -337,6 +337,7 @@ SUBDIR+=	ccrypt
 SUBDIR+=	cdbfasta
 SUBDIR+=	cddlib
 SUBDIR+=	cde
+SUBDIR+=	cdhit
 SUBDIR+=	cdirip
 SUBDIR+=	cdogs
 SUBDIR+=	cdpr
diff --git a/cdhit/DESCR b/cdhit/DESCR
new file mode 100644
index 0000000000..06848d6e15
--- /dev/null
+++ b/cdhit/DESCR
@@ -0,0 +1,2 @@
+CD-HIT is a very widely used program for clustering and comparing protein or
+nucleotide sequences.
diff --git a/cdhit/Makefile b/cdhit/Makefile
new file mode 100644
index 0000000000..d2e1844063
--- /dev/null
+++ b/cdhit/Makefile
@@ -0,0 +1,44 @@
+# $NetBSD: Makefile,v 1.2 2016/07/09 06:37:51 wiz Exp $
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	cdhit-4.6.8
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=weizhongli/}
+GITHUB_TAG=	V${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://weizhong-lab.ucsd.edu/cd-hit/
+COMMENT=	Clustering and comparing protein or nucleotide sequences
+LICENSE=	gnu-gpl-v2
+
+USE_LANGUAGES=	c++
+USE_TOOLS+=	bash:run gmake perl
+REPLACE_PERL=	*.pl
+
+# Restore default overridden by GITHUB_TAG
+WRKSRC=		${WRKDIR}/${DISTNAME}
+
+SUBST_CLASSES+=		compiler
+SUBST_STAGE.compiler=	post-patch
+SUBST_MESSAGE.compiler=	Fixing hardcoded compiler name
+SUBST_FILES.compiler=	${MAKE_FILE}
+SUBST_SED.compiler=	-e 's|g++|${CXX:Q}|g'
+
+SUBST_CLASSES+=		bash
+SUBST_STAGE.bash=	post-patch
+SUBST_MESSAGE.bash=	Fixing bash path
+SUBST_FILES.bash=	cd-hit-2d-para.pl cd-hit-para.pl
+SUBST_SED.bash=		-e 's|/bin/bash|${PREFIX}/bin/bash|g'
+
+MAKE_FLAGS+=		openmp=yes PREFIX=${DESTDIR}${PREFIX}/bin
+
+DOCDIR=			${PREFIX}/share/doc/cdhit
+INSTALLATION_DIRS+=	bin ${DOCDIR}
+
+post-install:
+	${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR}
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/cdhit/PLIST b/cdhit/PLIST
new file mode 100644
index 0000000000..db374c4071
--- /dev/null
+++ b/cdhit/PLIST
@@ -0,0 +1,38 @@
+@comment $NetBSD$
+bin/FET.pl
+bin/cd-hit
+bin/cd-hit-2d
+bin/cd-hit-2d-para.pl
+bin/cd-hit-454
+bin/cd-hit-div
+bin/cd-hit-div.pl
+bin/cd-hit-est
+bin/cd-hit-est-2d
+bin/cd-hit-para.pl
+bin/clstr2tree.pl
+bin/clstr2txt.pl
+bin/clstr2xml.pl
+bin/clstr_cut.pl
+bin/clstr_list.pl
+bin/clstr_list_sort.pl
+bin/clstr_merge.pl
+bin/clstr_merge_noorder.pl
+bin/clstr_quality_eval.pl
+bin/clstr_quality_eval_by_link.pl
+bin/clstr_reduce.pl
+bin/clstr_renumber.pl
+bin/clstr_rep.pl
+bin/clstr_reps_faa_rev.pl
+bin/clstr_rev.pl
+bin/clstr_select.pl
+bin/clstr_select_rep.pl
+bin/clstr_size_histogram.pl
+bin/clstr_size_stat.pl
+bin/clstr_sort_by.pl
+bin/clstr_sort_prot_by.pl
+bin/clstr_sql_tbl.pl
+bin/clstr_sql_tbl_sort.pl
+bin/make_multi_seq.pl
+bin/plot_2d.pl
+bin/plot_len1.pl
+share/doc/cdhit/cdhit-user-guide.pdf
diff --git a/cdhit/distinfo b/cdhit/distinfo
new file mode 100644
index 0000000000..d8842f186b
--- /dev/null
+++ b/cdhit/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (cdhit-4.6.8.tar.gz) = 2461b9e00069e2317394c7eae32ac5523777d975
+RMD160 (cdhit-4.6.8.tar.gz) = 3519fd8e6551762eaafeaa9d699acd47e9972b3f
+SHA512 (cdhit-4.6.8.tar.gz) = 6f25780557ea119d12db301d16038fc2b5740f33953dae40216392574bd8bdd93c69c10ecb46a9159070e701d9f743e02cf46d80557faa6d407aec6d08f6e10c
+Size (cdhit-4.6.8.tar.gz) = 932535 bytes