| Port details |
- star Spliced Transcripts Alignment to a Reference
- 2.7.11.a_1 biology
 =2      2.7.11.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: 2024-05-05 14:58:47
- Commit Hash: 94ae9822
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/alexdobin/STAR
- 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
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: rna-STAR
- Flavors: there is no flavor information for this port.
- NOT_FOR_ARCHS: armv6 armv7 i386 mips powerpc powerpcspe
- distinfo:
- TIMESTAMP = 1692285897
SHA256 (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a
SIZE (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 12463429
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- xxd : sysutils/xxd
- gmake>=4.4.1 : devel/gmake
- gcc13 : lang/gcc13
- as : devel/binutils
- Runtime dependencies:
-
- gcc13 : lang/gcc13
- Library dependencies:
-
- libhts.so : biology/htslib
- This port is required by:
- for Run
-
- biology/rna-seq
Configuration Options:- No options to configure
- Options name:
- biology_star
- USES:
- compiler:c++11-lang gmake localbase:ldflags
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.7.11.a_1
05 May 2024 14:58:47
 |
Jason W. Bacon (jwb) |
biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
Reduces I/O during builds
PR: 278751
Reported by: diizzy |
2.7.11.a_1
21 Aug 2023 14:33:20
|
Jason W. Bacon (jwb) |
biology/star: Fix SIMD issue on non-amd64
Also remove some extraneous build flags from upstream Makefile
PR: 273240
Reported by: dizzy |
2.7.11.a
19 Aug 2023 21:51:47
|
Piotr Kubaj (pkubaj) |
biology/star: fix build on !amd64
The port tries to force AVX2, but it's only available on amd64. |
2.7.11.a
17 Aug 2023 16:01:09
|
Jason W. Bacon (jwb) |
biology/star: Update to 2.7.11a
A few bug fixes and new features
Add USE_GCC as a temporary hack for input read issue
This was also an issue in 2.7.10b
Changes: https://github.com/alexdobin/STAR/releases |
2.7.10.b
22 Jul 2023 20:59:59
|
Jason W. Bacon (jwb) |
biology/star: Set NOT_FOR_ARCHS to all 32-bit processors |
2.7.10.b
21 Jul 2023 16:21:29
|
Jason W. Bacon (jwb) |
biology/star: Update to 2.7.10b
Numerous fixes and enhancements
Changes: https://github.com/alexdobin/STAR/releases |
2.7.9.a_1
06 Jan 2023 01:27:16
|
Jason W. Bacon (jwb) |
biology/star: Bump PORTREVISION for biology/htslib update |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
2.7.9.a
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
2.7.9.a
24 Jul 2022 01:24:10
|
Yuri Victorovich (yuri) |
biology/star: Broken on systems where OpenMP isn't enabled
Reported by: fallout
Approved by: portmgr (blanket) |
2.7.9.a
26 Nov 2021 21:57:02
|
Jason W. Bacon (jwb) |
biology/star: Update to 2.7.9a
Also unbundle htslib
Changes: https://github.com/alexdobin/STAR/releases/tag/2.7.9a |
2.7.3.a_1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.7.3.a_1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.7.3.a_1
11 Jan 2021 17:39:52
 |
jwb |
biology/star: Drop dependency on gcc
Replace compiler:openmp with compiler:c++11-lang and localbase
PR: port/247753, ports/252379 |
2.7.3.a
09 Apr 2020 12:43:03
|
jwb |
biology/star: Upgrade to 2.7.3a
Several compatibility and feature enhancements |
2.7.2.d
06 Oct 2019 22:18:31
|
jwb |
biology/star: Upgrade to 2.7.2d
Fix chimeric output bug.
Numerous other minor fixes and enhancements since 2.7.0.
Reported by: portscout |
2.7.0.f_1
26 Jul 2019 20:46:57
|
gerald |
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 |
2.7.0.f
02 May 2019 00:39:51
|
jwb |
biology/star: Force newer GCC on platforms with GCC 4.2 base
PR: 237700
Submitted by: pkubaj |
2.7.0.f
23 Apr 2019 15:03:29
|
jwb |
biology/star: Modify PKGBASE to avoid conflict with archivers/star |
2.7.0.f
21 Apr 2019 20:30:56
|
jwb |
biology/star: Spliced Transcripts Alignment to a Reference
STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc. |
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