biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15516

5 files changed, 64 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index a885710258b7..3b59dc0c3090 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -19,6 +19,7 @@
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
     SUBDIR += chemeq
+    SUBDIR += clustal-omega
     SUBDIR += clustalw
     SUBDIR += clustalx
     SUBDIR += consed
diff --git a/biology/clustal-omega/Makefile b/biology/clustal-omega/Makefile
new file mode 100644
index 000000000000..c258ec31559f
--- /dev/null
+++ b/biology/clustal-omega/Makefile
@@ -0,0 +1,20 @@
+# $FreeBSD$
+
+PORTNAME=	clustal-omega
+DISTVERSION=	1.2.4
+CATEGORIES=	biology
+MASTER_SITES=	http://www.clustal.org/omega/
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Multiple alignment of nucleic acid and protein, replaces clustalw
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+LIB_DEPENDS=	libargtable2.so:devel/argtable
+
+USES=		libtool localbase
+
+GNU_CONFIGURE=	yes
+
+.include <bsd.port.mk>
diff --git a/biology/clustal-omega/distinfo b/biology/clustal-omega/distinfo
new file mode 100644
index 000000000000..f0a0f6887699
--- /dev/null
+++ b/biology/clustal-omega/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1526846209
+SHA256 (clustal-omega-1.2.4.tar.gz) = 8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee
+SIZE (clustal-omega-1.2.4.tar.gz) = 1170516
diff --git a/biology/clustal-omega/pkg-descr b/biology/clustal-omega/pkg-descr
new file mode 100644
index 000000000000..7c4ad1d69b44
--- /dev/null
+++ b/biology/clustal-omega/pkg-descr
@@ -0,0 +1,8 @@
+Clustal Omega is the latest addition to the Clustal family. It offers a
+significant increase in scalability over previous versions, allowing hundreds
+of thousands of sequences to be aligned in only a few hours. It will also make
+use of multiple processors, where present. In addition, the quality of
+alignments is superior to previous versions, as measured by a range of popular
+benchmarks.
+
+WWW: http://www.clustal.org/omega/
diff --git a/biology/clustal-omega/pkg-plist b/biology/clustal-omega/pkg-plist
new file mode 100644
index 000000000000..965f21ae3d7c
--- /dev/null
+++ b/biology/clustal-omega/pkg-plist
@@ -0,0 +1,32 @@
+bin/clustalo
+include/clustalo/clustal-omega-config.h
+include/clustalo/clustal-omega.h
+include/clustalo/clustal/hhalign_wrapper.h
+include/clustalo/clustal/ktuple_pair.h
+include/clustalo/clustal/log.h
+include/clustalo/clustal/mbed.h
+include/clustalo/clustal/muscle_tree.h
+include/clustalo/clustal/pair_dist.h
+include/clustalo/clustal/progress.h
+include/clustalo/clustal/seq.h
+include/clustalo/clustal/symmatrix.h
+include/clustalo/clustal/tree.h
+include/clustalo/clustal/util.h
+include/clustalo/clustal/weights.h
+include/clustalo/hhalign/general.h
+include/clustalo/hhalign/hhfunc.h
+include/clustalo/squid/gki.h
+include/clustalo/squid/gsi64.h
+include/clustalo/squid/msa.h
+include/clustalo/squid/rk.h
+include/clustalo/squid/sqfuncs.h
+include/clustalo/squid/squid.h
+include/clustalo/squid/sre_random.h
+include/clustalo/squid/ssi.h
+include/clustalo/squid/stockholm.h
+include/clustalo/squid/stopwatch.h
+include/clustalo/squid/vectorops.h
+include/clustalo/squid/version.h
+lib/libclustalo.a
+libdata/pkgconfig/clustalo.pc
+%%DOCSDIR%%/README