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New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes

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This commit is contained in:
Yuri Victorovich 2019-02-03 18:08:14 +00:00
parent 3b63ab6bbf
commit a1bcae4a2a
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=492058
4 changed files with 51 additions and 0 deletions
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1
biology/Makefile
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@ -101,6 +101,7 @@
SUBDIR += phyml
SUBDIR += plinkseq
SUBDIR += primer3
SUBDIR += prodigal
SUBDIR += protomol
SUBDIR += psi88
SUBDIR += py-Genesis-PyAPI

25
biology/prodigal/Makefile Normal file
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@ -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 <bsd.port.mk>

3
biology/prodigal/distinfo Normal file
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@ -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

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biology/prodigal/pkg-descr Normal file
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@ -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