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| author | yuri <yuri@FreeBSD.org> | 2019-02-04 02:08:14 +0800 |
|---|---|---|
| committer | yuri <yuri@FreeBSD.org> | 2019-02-04 02:08:14 +0800 |
| commit | f8d2b2037f1df436fefb591e28c861ee138db3e7 (patch) | |
| tree | 9096581411028d4da9c755d2aa04e1f23a0461f3 /biology | |
| parent | 87c0b63bde9002e8aeef496c105322844bc83704 (diff) | |
| download | freebsd-ports-gnome-f8d2b2037f1df436fefb591e28c861ee138db3e7.tar.gz freebsd-ports-gnome-f8d2b2037f1df436fefb591e28c861ee138db3e7.tar.zst freebsd-ports-gnome-f8d2b2037f1df436fefb591e28c861ee138db3e7.zip | |
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/prodigal/Makefile | 25 | ||||
| -rw-r--r-- | biology/prodigal/distinfo | 3 | ||||
| -rw-r--r-- | biology/prodigal/pkg-descr | 22 |
4 files changed, 51 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index bf5f4af2c23c..75eb9e66c060 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -101,6 +101,7 @@ SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 + SUBDIR += prodigal SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI diff --git a/biology/prodigal/Makefile b/biology/prodigal/Makefile new file mode 100644 index 000000000000..c227b6a80f17 --- /dev/null +++ b/biology/prodigal/Makefile @@ -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> diff --git a/biology/prodigal/distinfo b/biology/prodigal/distinfo new file mode 100644 index 000000000000..f2c70fef6b3f --- /dev/null +++ b/biology/prodigal/distinfo @@ -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 diff --git a/biology/prodigal/pkg-descr b/biology/prodigal/pkg-descr new file mode 100644 index 000000000000..7d9eb1c4c855 --- /dev/null +++ b/biology/prodigal/pkg-descr @@ -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 |