git: a7eec55e9ca0 - main - biology/barrnap: New port: BAsic Rapid Ribosomal RNA Predictor

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=a7eec55e9ca07d154f1de127c3ecc6187bce06d6

commit a7eec55e9ca07d154f1de127c3ecc6187bce06d6
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-11-25 03:08:04 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-11-25 03:08:42 +0000

    biology/barrnap: New port: BAsic Rapid Ribosomal RNA Predictor
---
 biology/Makefile          |  1 +
 biology/barrnap/Makefile  | 32 ++++++++++++++++++++++++++++++++
 biology/barrnap/distinfo  |  3 +++
 biology/barrnap/pkg-descr |  6 ++++++
 biology/barrnap/pkg-plist |  5 +++++
 5 files changed, 47 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 2ba55e0738ae..a4b704020908 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -7,6 +7,7 @@
     SUBDIR += babel
     SUBDIR += bamtools
     SUBDIR += bamutil
+    SUBDIR += barrnap
     SUBDIR += bbmap
     SUBDIR += bcftools
     SUBDIR += bedtools
diff --git a/biology/barrnap/Makefile b/biology/barrnap/Makefile
new file mode 100644
index 000000000000..90971ff06d7a
--- /dev/null
+++ b/biology/barrnap/Makefile
@@ -0,0 +1,32 @@
+PORTNAME=	barrnap
+DISTVERSION=	0.9
+CATEGORIES=	biology science
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	BAsic Rapid Ribosomal RNA Predictor
+WWW=		https://github.com/tseemann/barrnap
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+RUN_DEPENDS=	bedtools:biology/bedtools \
+		nhmmer:biology/hmmer
+
+USES=		gmake perl5
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	tseemann
+
+NO_BUILD=	yes
+NO_ARCH=	yes
+
+TEST_TARGET=	test
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/bin/barrnap ${STAGEDIR}${PREFIX}/bin
+	cd ${WRKSRC} && ${COPYTREE_SHARE} db ${STAGEDIR}${DATADIR}
+	${REINPLACE_CMD} \
+		-i '' -e 's|^my $$DBDIR = .*|my $$DBDIR = "${DATADIR}/db";|' \
+		${STAGEDIR}${PREFIX}/bin/barrnap
+
+.include <bsd.port.mk>
diff --git a/biology/barrnap/distinfo b/biology/barrnap/distinfo
new file mode 100644
index 000000000000..48b3f9e21728
--- /dev/null
+++ b/biology/barrnap/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1669343398
+SHA256 (tseemann-barrnap-0.9_GH0.tar.gz) = 36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15
+SIZE (tseemann-barrnap-0.9_GH0.tar.gz) = 11837541
diff --git a/biology/barrnap/pkg-descr b/biology/barrnap/pkg-descr
new file mode 100644
index 000000000000..bec4ff368560
--- /dev/null
+++ b/biology/barrnap/pkg-descr
@@ -0,0 +1,6 @@
+SIMD-vectorized implementation of the Viterbi algorithm for profile HMM
+alignment and introduced various other speed-ups. This accelerated HHsearch by a
+factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is
+~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch
+and HHblits searches with many query profile HMMs can be parallelized over cores
+and over servers in a cluster using OpenMP and message passing interface (MPI).
diff --git a/biology/barrnap/pkg-plist b/biology/barrnap/pkg-plist
new file mode 100644
index 000000000000..fbf0ddaac319
--- /dev/null
+++ b/biology/barrnap/pkg-plist
@@ -0,0 +1,5 @@
+bin/barrnap
+%%DATADIR%%/db/arc.hmm
+%%DATADIR%%/db/bac.hmm
+%%DATADIR%%/db/euk.hmm
+%%DATADIR%%/db/mito.hmm