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Sun, 3 Feb 2019 18:08:15 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x13I8FiV020303; Sun, 3 Feb 2019 18:08:15 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x13I8EJb020299; Sun, 3 Feb 2019 18:08:14 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201902031808.x13I8EJb020299@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 3 Feb 2019 18:08:14 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r492058 - in head/biology: . prodigal X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . prodigal X-SVN-Commit-Revision: 492058 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: C41B9805AC X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.96 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.96)[-0.961,0]; NEURAL_HAM_LONG(-1.00)[-0.999,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 03 Feb 2019 18:08:16 -0000 Author: yuri Date: Sun Feb 3 18:08:14 2019 New Revision: 492058 URL: https://svnweb.freebsd.org/changeset/ports/492058 Log: New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes Added: head/biology/prodigal/ head/biology/prodigal/Makefile (contents, props changed) head/biology/prodigal/distinfo (contents, props changed) head/biology/prodigal/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Feb 3 17:28:37 2019 (r492057) +++ head/biology/Makefile Sun Feb 3 18:08:14 2019 (r492058) @@ -101,6 +101,7 @@ SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 + SUBDIR += prodigal SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI Added: head/biology/prodigal/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/prodigal/Makefile Sun Feb 3 18:08:14 2019 (r492058) @@ -0,0 +1,25 @@ +# $FreeBSD$ + +PORTNAME= prodigal +DISTVERSIONPREFIX= v +DISTVERSION= 2.6.3-2 +DISTVERSIONSUFFIX= -gfe80417 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Protein-coding gene prediction for prokaryotic genomes + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= gmake +USE_GITHUB= yes +GH_ACCOUNT= hyattpd +GH_PROJECT= Prodigal + +BINARY_ALIAS= gcc=${CC} +MAKE_ARGS= INSTALLDIR=${STAGEDIR}${PREFIX}/bin + +PLIST_FILES= bin/${PORTNAME} + +.include Added: head/biology/prodigal/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/prodigal/distinfo Sun Feb 3 18:08:14 2019 (r492058) @@ -0,0 +1,3 @@ +TIMESTAMP = 1549215427 +SHA256 (hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz) = a8229a3ce38f7d6553730d5a5d3c46c619abd502de8527cb175e9af022c3b371 +SIZE (hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz) = 611025 Added: head/biology/prodigal/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/prodigal/pkg-descr Sun Feb 3 18:08:14 2019 (r492058) @@ -0,0 +1,22 @@ +Fast, reliable protein-coding gene prediction for prokaryotic genomes. + +Features: +* Predicts protein-coding genes: Prodigal provides fast, accurate protein-coding + gene predictions in GFF3, Genbank, or Sequin table format. +* Handles draft genomes and metagenomes: Prodigal runs smoothly on finished + genomes, draft genomes, and metagenomes. +* Runs quickly: Prodigal analyzes the E. coli K-12 genome in 10 seconds on a + modern MacBook Pro. +* Runs unsupervised: Prodigal is an unsupervised machine learning algorithm. It + does not need to be provided with any training data, and instead automatically + learns the properties of the genome from the sequence itself, including RBS + motif usage, start codon usage, and coding statistics. +* Handles gaps and partial genes: The user can specify if Prodigal should build + genes across runs of N's as well as how to handle genes at the edges of + contigs. +* Identifies translation initiation sites: Prodigal predicts the correct + translation initiation site for most genes, and can output information about + every potential start site in the genome, including confidence score, RBS + motif, and much more. + +WWW: https://github.com/hyattpd/Prodigal