BSD Ports

biology/gffread 0.12.9 FreeBSD

GFF/GTF format conversions, filtering, FASTA extraction, etc

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
MIT
Categories
biology
Package size
111.7 KiB, 284.3 KiB installed

Description

GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. The program gffread can be used to validate, filter, convert and perform various other operations on GFF files. Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs.

In the other systems

SystemPortVersion
FreeBSDbiology/gffread0.12.9
NetBSDbiology/gffread0.12.7
DragonFlybiology/gffread0.12.7
HardenedBSDbiology/gffread0.12.9
GhostBSDbiology/gffread0.12.9

Install

Binary package:

pkg install gffread

From the ports tree:

cd /usr/ports/biology/gffread/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	gffread>0:biology/gffread

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest0.12.90.12.90.12.70.12.70.12.9
FreeBSD:14:quarterly0.12.90.12.9n/a0.12.70.12.9
FreeBSD:15:latest0.12.90.12.9n/a0.12.70.12.7
FreeBSD:15:quarterly0.12.90.12.9n/an/an/a
FreeBSD:16:latest0.12.90.12.9n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Build dependencies 3

Configuration

No options to configure.

USES
gmake
Service scripts
none
Conflicts with
cufflinks

Files

distinfo 2
FileSizeSHA256
gpertea-gffread-v0.12.9_GH0.tar.gz40871092eb4a52fdd14c5fd3684041ef2d040c44d7414d076467a326eea2efa087a085
gpertea-gclib-v0.12.8_GH0.tar.gz262545a8dea4d273d6802f77f26a5394b1d66dfc1aba46a725c61e4c7399b756fb75e3

Commit history 1

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.