- star Spliced Transcripts Alignment to a Reference
- 2.7.3.a_1 biology =0 2.7.3.a_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-04-21 20:31:13
- Last Update: 2021-04-07 08:09:01
- Commit Hash: cf118cc
- License: GPLv3
- 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
- SVNWeb : git : Homepage
- pkg-plist: as obtained via:
- Dependency lines:
- To install the port: cd /usr/ports/biology/star/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/star
- pkg install rna-STAR
- PKGNAME: rna-STAR
- Flavors: there is no flavor information for this port.
- NOT_FOR_ARCHS: i386 powerpc
- TIMESTAMP = 1586376571
SHA256 (alexdobin-STAR-2.7.3a_GH0.tar.gz) = de204175351dc5f5ecc40cf458f224617654bdb8e00df55f0bb03a5727bf26f9
SIZE (alexdobin-STAR-2.7.3a_GH0.tar.gz) = 8550987
- Packages (timestamps in pop-ups are UTC):
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
- gmake>=4.3 : devel/gmake
- There are no ports dependent upon this port
- Configuration Options:
- No options to configure
- Options name:
- compiler:c++11-lang gmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|Commit History - (may be incomplete: see SVNWeb link above for full details)
|07 Apr 2021 08:09:01
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
|06 Apr 2021 14:31:07
Remove # $FreeBSD$ from Makefiles.
|11 Jan 2021 17:39:52
biology/star: Drop dependency on gcc
Replace compiler:openmp with compiler:c++11-lang and localbase
PR: port/247753, ports/252379
|09 Apr 2020 12:43:03
biology/star: Upgrade to 2.7.3a
Several compatibility and feature enhancements
|06 Oct 2019 22:18:31
biology/star: Upgrade to 2.7.2d
Fix chimeric output bug.
Numerous other minor fixes and enhancements since 2.7.0.
Reported by: portscout
|26 Jul 2019 20:46:57
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.
|02 May 2019 00:39:51
biology/star: Force newer GCC on platforms with GCC 4.2 base
Submitted by: pkubaj
|23 Apr 2019 15:03:29
biology/star: Modify PKGBASE to avoid conflict with archivers/star
|21 Apr 2019 20:30:56
biology/star: Spliced Transcripts Alignment to a Reference
STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.