| Port details |
- salmon Transcript-level quantification of RNA-seq from lightweight alignments
- 1.10.2_7 biology
 =2      1.10.2_6Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2023-07-21 23:09:07
- Last Update: 2025-02-14 03:17:22
- Commit Hash: fa53920
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/COMBINE-lab/salmon
- Description:
- Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. Salmon
achieves is accuracy and speed via a number of different innovations,
including the use of quasi-mapping (accurate but fast-to-compute
proxies for traditional read alignments), and massively-parallel
stochastic collapsed variational inference. The result is a versatile
tool that fits nicely into many differnt pipelines.
  ¦  ¦  ¦  ¦ 
- 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/salmon/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/salmon
- pkg install salmon
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: salmon
- Flavors: there is no flavor information for this port.
- NOT_FOR_ARCHS: armv6 armv7 i386 mips powerpc powerpcspe
- distinfo:
- TIMESTAMP = 1689958260
SHA256 (COMBINE-lab-salmon-v1.10.2_GH0.tar.gz) = 976989182160fef3afb4429ee8b85d8dd39ed6ca212bb14d6a65cde0e985fb98
SIZE (COMBINE-lab-salmon-v1.10.2_GH0.tar.gz) = 7193261
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:
-
- bash : shells/bash
- cereal>=1.3.0 : devel/cereal
- libgff==2.0.0 : biology/libgff
- libtool : devel/libtool
- autoreconf : devel/autoconf
- aclocal : devel/automake
- cmake : devel/cmake-core
- gmake>=4.4.1 : devel/gmake
- Library dependencies:
-
- libboost_system.so : devel/boost-libs
- libtbb.so : devel/onetbb
- libcurl.so : ftp/curl
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_salmon
- USES:
- cmake:noninja gmake localbase shebangfix
- 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 |
|---|
1.10.2_7
14 Feb 2025 03:17:22
 |
Dima Panov (fluffy) |
devel/boost: bump consumers after Boost-1.87 update
Sponsored by: Future Crew, LLC |
1.10.2_6
20 Nov 2024 10:05:25
|
Dima Panov (fluffy) |
devel/boost: bump consu,ers after update Boost to 1.86 release
Sponsored by: Future Crew, LLC |
1.10.2_5
03 Oct 2024 10:25:14
|
Dima Panov (fluffy) |
*/*: bump consumers after devel/boost* update
With hat: office
Sponsored by: Future Crew, LLC |
1.10.2_4
04 Jul 2024 11:39:44
|
Ganael LAPLANCHE (martymac) |
devel/onetbb: Update to 2021.13.0
and bump dependent ports' revisions.
Release
notes: https://github.com/oneapi-src/oneTBB/blob/v2021.13.0/RELEASE_NOTES.md |
1.10.2_3
17 Apr 2024 11:28:34
|
Ganael LAPLANCHE (martymac) |
devel/onetbb: Update to 2021.12.0
and bump dependent ports' revisions.
Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.12.0 |
1.10.2_2
12 Apr 2024 06:04:05
|
Mathieu Arnold (mat) |
cleanup: remove occurrences of WITH_DEBUG
DEBUG like all ports features, must not ever be set in a port, they are
user facing features, that the user needs to enable in their
environment/make.conf, either by defining WITH_DEBUG globally, or by
setting WITH_DEBUG_PORTS with origin of ports they want DEBUG enabled
in. |
1.10.2_2
28 Nov 2023 11:35:02
|
Ganael LAPLANCHE (martymac) |
devel/onetbb: Update to 2021.11.0
and bump dependent ports' revisions.
Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.11.0 |
1.10.2_1
21 Aug 2023 10:09:23
|
Ganael LAPLANCHE (martymac) |
devel/onetbb: Update to 2021.10.0
and bump dependent ports' revisions.
Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.10.0 |
1.10.2
22 Jul 2023 21:12:50
|
Jason W. Bacon (jwb) |
biology/salmon: Set NOT_FOR_ARCHS to all 32-bit processors |
1.10.2
21 Jul 2023 23:06:36
|
Jason W. Bacon (jwb) |
biology/salmon: Transcript-level quantification of RNA-seq
Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. Salmon
achieves is accuracy and speed via a number of different innovations,
including the use of quasi-mapping (accurate but fast-to-compute
proxies for traditional read alignments), and massively-parallel
stochastic collapsed variational inference. The result is a versatile
tool that fits nicely into many differnt pipelines. |
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