Import biology/cdhit as cdhit-4.6.4.

Packaged in pkgsrc-wip by Jason Bacon.

CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.

4 files changed, 86 insertions, 0 deletions

diff --git a/biology/cdhit/DESCR b/biology/cdhit/DESCR
new file mode 100644
index 00000000000..06848d6e151
--- /dev/null
+++ b/biology/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/biology/cdhit/Makefile b/biology/cdhit/Makefile
new file mode 100644
index 00000000000..96e7dbf51bb
--- /dev/null
+++ b/biology/cdhit/Makefile
@@ -0,0 +1,44 @@
+# $NetBSD: Makefile,v 1.1 2015/10/12 16:48:08 leot Exp $
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	cdhit-4.6.4
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=weizhongli/}
+GITHUB_TAG=	V${PKGVERSION_NOREV}
+
+MAINTAINER=	jwbacon@tds.net
+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/biology/cdhit/PLIST b/biology/cdhit/PLIST
new file mode 100644
index 00000000000..4dc806a7615
--- /dev/null
+++ b/biology/cdhit/PLIST
@@ -0,0 +1,35 @@
+@comment $NetBSD: PLIST,v 1.1 2015/10/12 16:48:08 leot Exp $
+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_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/biology/cdhit/distinfo b/biology/cdhit/distinfo
new file mode 100644
index 00000000000..3c484bb072c
--- /dev/null
+++ b/biology/cdhit/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2015/10/12 16:48:08 leot Exp $
+
+SHA1 (cdhit-4.6.4.tar.gz) = 3606a8200e62ac60c9dd782a57bec426256e6fa8
+RMD160 (cdhit-4.6.4.tar.gz) = a94a29103393dded87000173d8eb4ec1a1e0614f
+Size (cdhit-4.6.4.tar.gz) = 1148426 bytes