BSD Ports

biology/star 2.7.11.a_1 FreeBSD

Spliced Transcripts Alignment to a Reference

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
GPLv3
Categories
biology
Package size
544.9 KiB, 1379.7 KiB installed

Description

STAR (Spliced Transcripts Alignment to a Reference) aims to achieve accurate alignment of high-throughput RNA-seq data.

STAR is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 x 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision

In the other systems

SystemPortVersion
FreeBSDbiology/star2.7.11.a_1
DragonFlybiology/star2.7.9.a

Install

Binary package:

pkg install rna-STAR

From the ports tree:

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

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

RUN_DEPENDS=	rna-STAR>0:biology/star

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:latest2.7.11.a_12.7.11.a_1---
FreeBSD:14:quarterly2.7.11.a_12.7.11.a_1n/a--
FreeBSD:15:latest2.7.11.a_12.7.11.a_1n/a--
FreeBSD:15:quarterly2.7.11.a_12.7.11.a_1n/an/an/a
FreeBSD:16:latest2.7.11.a_12.7.11.a_1n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Library 1

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

Build dependencies 20
Run dependencies 17
Required by 1

Configuration

No options to configure.

USES
compiler:c++11-lang gmake localbase:ldflags
Service scripts
none

Message after installing

===>   NOTICE:

The rna-STAR port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

distinfo 1
FileSizeSHA256
alexdobin-STAR-2.7.11a_GH0.tar.gz1.2463429e+07542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a

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.