5 files changed, 116 insertions, 0 deletions

diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile
new file mode 100644
index 000000000000..3500844d5c9b
--- /dev/null
+++ b/biology/infernal/Makefile
@@ -0,0 +1,46 @@
+# $FreeBSD$
+
+PORTNAME=	infernal
+PORTVERSION=	1.1.2
+CATEGORIES=	biology
+MASTER_SITES=	http://eddylab.org/infernal/
+
+MAINTAINER=	mzaki@niid.go.jp
+COMMENT=	Search sequence databases for structural RNA homologs
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+ONLY_FOR_ARCHS=	amd64 i386
+ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
+
+USES=		gmake
+GNU_CONFIGURE=	yes
+MAKE_ARGS=	V=1
+
+DOCFILES=	Userguide.pdf
+EXAMPLES=	5S_rRNA.c.cm 5S_rRNA.sto \
+		Cobalamin.c.cm Cobalamin.fa Cobalamin.sto \
+		metag-example.fa minifam-metag.out minifam.cm \
+		minifam.cm.i1f minifam.cm.i1i minifam.cm.i1m minifam.cm.i1p \
+		mrum-genome.fa mrum-tRNAs10.fa mrum-tRNAs10.out \
+		tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \
+		tRNA5-noss.sto tRNA5.c.cm tRNA5.sto
+
+OPTIONS_DEFINE=	DOCS EXAMPLES TEST
+
+TEST_TEST_TARGET=	check
+TEST_USES=	shebangfix perl5
+TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build
+
+post-build-TEST-on:	do-test
+
+post-install-DOCS-on:
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
+
+post-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR}
+
+.include <bsd.port.mk>
diff --git a/biology/infernal/distinfo b/biology/infernal/distinfo
new file mode 100644
index 000000000000..a99bece6070f
--- /dev/null
+++ b/biology/infernal/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1528251928
+SHA256 (infernal-1.1.2.tar.gz) = ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b
+SIZE (infernal-1.1.2.tar.gz) = 19364073
diff --git a/biology/infernal/files/patch-configure b/biology/infernal/files/patch-configure
new file mode 100644
index 000000000000..f9fdfd5f3f0d
--- /dev/null
+++ b/biology/infernal/files/patch-configure
@@ -0,0 +1,10 @@
+--- configure.orig	2016-07-01 20:26:34 UTC
++++ configure
+@@ -3855,6 +3855,7 @@ fi
+ if test "$impl_choice" = "none"; then
+   case $host in
+     ia64-*-*)      impl_choice=sse;;
++    amd64-*-*)     impl_choice=sse;;
+     i?86-*-*)      impl_choice=sse;;
+     x86*-*-*)      impl_choice=sse;;
+     powerpc*-*-*)  impl_choice=vmx;;
diff --git a/biology/infernal/pkg-descr b/biology/infernal/pkg-descr
new file mode 100644
index 000000000000..7436fa4f7d8f
--- /dev/null
+++ b/biology/infernal/pkg-descr
@@ -0,0 +1,14 @@
+Infernal, standing for "INFERence of RNA ALignment", is a tool for searching
+DNA sequence database for RNA structure and sequence similarities.
+
+It is based on Covariance Model (CM), which scores a combination of sequence
+consensus and RNA secondary structure consensus, and thus is more capable of
+identifying RNA homologs than using primary sequence profile.
+
+The Rfam database of RNA families is based on Infernal. 
+
+Citation:
+Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches,
+Bioinformatics 29: 2933-2935.
+
+WWW: http://eddylab.org/infernal/
diff --git a/biology/infernal/pkg-plist b/biology/infernal/pkg-plist
new file mode 100644
index 000000000000..770ce65d633d
--- /dev/null
+++ b/biology/infernal/pkg-plist
@@ -0,0 +1,43 @@
+bin/cmalign
+bin/cmbuild
+bin/cmcalibrate
+bin/cmconvert
+bin/cmemit
+bin/cmfetch
+bin/cmpress
+bin/cmscan
+bin/cmsearch
+bin/cmstat
+man/man1/cmalign.1.gz
+man/man1/cmbuild.1.gz
+man/man1/cmcalibrate.1.gz
+man/man1/cmconvert.1.gz
+man/man1/cmemit.1.gz
+man/man1/cmfetch.1.gz
+man/man1/cmpress.1.gz
+man/man1/cmscan.1.gz
+man/man1/cmsearch.1.gz
+man/man1/cmstat.1.gz
+man/man1/infernal.1.gz
+%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5S_rRNA.c.cm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5S_rRNA.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.c.cm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/metag-example.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam-metag.out
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1f
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1i
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1m
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1p
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-genome.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.out
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.c.cm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-mrum.out
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-noss.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5.c.cm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5.sto