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Fri, 25 Nov 2022 03:08:45 GMT (envelope-from git) Date: Fri, 25 Nov 2022 03:08:45 GMT Message-Id: <202211250308.2AP38jMR034845@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: a7eec55e9ca0 - main - biology/barrnap: New port: BAsic Rapid Ribosomal RNA Predictor List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: a7eec55e9ca07d154f1de127c3ecc6187bce06d6 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=a7eec55e9ca07d154f1de127c3ecc6187bce06d6 commit a7eec55e9ca07d154f1de127c3ecc6187bce06d6 Author: Yuri Victorovich AuthorDate: 2022-11-25 03:08:04 +0000 Commit: Yuri Victorovich 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 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