star Spliced Transcripts Alignment to a Reference

2.7.2.d biology =0 2.7.0.fVersion of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2019-04-21 20:31:13

Last Update: 2019-10-06 23:18:31

SVN Revision: 513915

License: GPLv3

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 WWW: https://github.com/alexdobin/STAR

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (4 items)

1. bin/STAR
2. /usr/local/share/licenses/rna-STAR-2.7.2.d/catalog.mk
3. /usr/local/share/licenses/rna-STAR-2.7.2.d/LICENSE
4. /usr/local/share/licenses/rna-STAR-2.7.2.d/GPLv3

Collapse this list.

Dependency lines:

• rna-STAR>0:biology/star

To install the port: cd /usr/ports/biology/star/ && make install clean

To add the package: pkg install rna-STAR

PKGNAME: rna-STAR

Flavors: there is no flavor information for this port.

NOT_FOR_ARCHS: i386 powerpc

distinfo:

TIMESTAMP = 1570398385 SHA256 (alexdobin-STAR-2.7.2d_GH0.tar.gz) = 46eba14658082c93d7982c5b5898051c7139f1f9add9390de7c135f587b42ab4 SIZE (alexdobin-STAR-2.7.2d_GH0.tar.gz) = 8142737

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. gmake : devel/gmake
2. gcc9 : lang/gcc9
3. as : devel/binutils

Runtime dependencies:

1. gcc9 : lang/gcc9

There are no ports dependent upon this port

Configuration Options

No options to configure

USES:

compiler:openmp gmake

Master Sites:

1. https://codeload.github.com/alexdobin/STAR/tar.gz/2.7.2d?dummy=/

biology/star: Upgrade to 2.7.2d

Fix chimeric output bug.

Numerous other minor fixes and enhancements since 2.7.0.

Reported by:    portscout

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

biology/star: Force newer GCC on platforms with GCC 4.2 base

PR:             237700
Submitted by:   pkubaj

biology/star: Modify PKGBASE to avoid conflict with archivers/star

biology/star: Spliced Transcripts Alignment to a Reference

STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.

4 vulnerabilities affecting 12 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2019-10-19 10:52:46