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Port details
salmon Transcript-level quantification of RNA-seq from lightweight alignments
1.10.3_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.10.3_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-07-21 23:09:07
Last Update: 2026-03-10 23:03:35
Commit Hash: faadb58
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/salmon
  2. /usr/local/share/licenses/salmon-1.10.3_2/catalog.mk
  3. /usr/local/share/licenses/salmon-1.10.3_2/LICENSE
  4. /usr/local/share/licenses/salmon-1.10.3_2/GPLv3
Collapse this list.
USE_RC_SUBR (Service Scripts)
  • no SUBR information found for this port
Dependency lines:
  • salmon>0:biology/salmon
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 = 1753565795 SHA256 (COMBINE-lab-salmon-v1.10.3_GH0.tar.gz) = a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871 SIZE (COMBINE-lab-salmon-v1.10.3_GH0.tar.gz) = 7193092

Expand this list (6 items)

Collapse this list.

SHA256 (COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz) = 5d345ba30f22ff4448f4bf2920d2246a11cc38b203e12828c07b2612e41d2951 SIZE (COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz) = 3368105 SHA256 (jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz) = 5fef32bb10991b388b4a92292e58d6ef8e7eda812ab2d6a10daaca9a757e6302 SIZE (jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz) = 3381908 SHA256 (samtools-htscodecs-de42211_GH0.tar.gz) = 65e632bf00e2e456a3040e8a4748dbd33161595029ba49dec89d5301ebdd4de6 SIZE (samtools-htscodecs-de42211_GH0.tar.gz) = 3200933

Collapse this list.

Packages (timestamps in pop-ups are UTC):
salmon
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.10.3_21.10.3_2---n/an/an/a
FreeBSD:13:quarterly1.10.3_11.10.3_1---n/an/an/a
FreeBSD:14:latest1.10.3_21.10.3_2------
FreeBSD:14:quarterly1.10.3_11.10.3_1------
FreeBSD:15:latest1.10.3_21.10.3_2n/a-n/an/a--
FreeBSD:15:quarterly1.10.3_11.10.3_1n/a-n/an/a--
FreeBSD:16:latest1.10.3_21.10.3_2n/a-n/an/a--
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. cereal>=1.3.0 : devel/cereal
  3. libgff>=2.0.0 : biology/libgff
  4. libtool : devel/libtool
  5. autoreconf : devel/autoconf
  6. aclocal : devel/automake
  7. eigen>0 : math/eigen3
  8. libdivide>0 : math/libdivide
  9. curl>0 : ftp/curl
  10. cmake : devel/cmake-core
  11. gmake>=4.4.1 : devel/gmake
Library dependencies:
  1. libtbb.so : devel/onetbb
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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.3?dummy=/
Collapse this list.

Number of commits found: 15

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.10.3_2
10 Mar 2026 23:03:35
commit hash: faadb5898d6485975074edef381765678edd700fcommit hash: faadb5898d6485975074edef381765678edd700fcommit hash: faadb5898d6485975074edef381765678edd700fcommit hash: faadb5898d6485975074edef381765678edd700f files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/salmon: Unbreak: Relax libgff version requirement

Also drop unnecessary libboost dep

Reported by:    pkg-fallout
1.10.3_1
18 Dec 2025 14:58:08
commit hash: 0729671e31677625693578f8a890e7a5ad555b7fcommit hash: 0729671e31677625693578f8a890e7a5ad555b7fcommit hash: 0729671e31677625693578f8a890e7a5ad555b7fcommit hash: 0729671e31677625693578f8a890e7a5ad555b7f files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
*: WITH_DEBUG is a user feature not a port one
1.10.3_1
20 Oct 2025 11:48:39
commit hash: 67fb95fb3bd5e61957877f5ac31cd790bff786b5commit hash: 67fb95fb3bd5e61957877f5ac31cd790bff786b5commit hash: 67fb95fb3bd5e61957877f5ac31cd790bff786b5commit hash: 67fb95fb3bd5e61957877f5ac31cd790bff786b5 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost: bump consumers after boost upgrade (+)

Get rid of direct dependency ob libbost_system.so, use libboost_thread.so
instead
1.10.3
27 Jul 2025 21:04:26
commit hash: ace12788b0dbb0a71c23a618c534595c96b44205commit hash: ace12788b0dbb0a71c23a618c534595c96b44205commit hash: ace12788b0dbb0a71c23a618c534595c96b44205commit hash: ace12788b0dbb0a71c23a618c534595c96b44205 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/salmon: Update to tag 1.10.3

Fix build under clang19:
    Patch out deprecated atomic template copy
    Unbundle eigen and libdivide
    https://github.com/COMBINE-lab/salmon/issues/988
Upstream updates to improve ARM support
Changes: https://github.com/COMBINE-lab/salmon/commits/master/

Reported by:    pkg-fallout
1.10.2_8
02 Jun 2025 00:40:43
commit hash: 18632db919ce49d62374e1020f0320153951f834commit hash: 18632db919ce49d62374e1020f0320153951f834commit hash: 18632db919ce49d62374e1020f0320153951f834commit hash: 18632db919ce49d62374e1020f0320153951f834 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost: bump consumers after Boost update
1.10.2_7
14 Feb 2025 03:17:22
commit hash: fa53920e7219d4246816f65034ad058e81de3353commit hash: fa53920e7219d4246816f65034ad058e81de3353commit hash: fa53920e7219d4246816f65034ad058e81de3353commit hash: fa53920e7219d4246816f65034ad058e81de3353 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost: bump consumers after Boost-1.87 update

Sponsored by:	Future Crew, LLC
1.10.2_6
20 Nov 2024 10:05:25
commit hash: 312ee18b022b4abcb14973bb10894ba152b8f60bcommit hash: 312ee18b022b4abcb14973bb10894ba152b8f60bcommit hash: 312ee18b022b4abcb14973bb10894ba152b8f60bcommit hash: 312ee18b022b4abcb14973bb10894ba152b8f60b files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
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
commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
*/*: bump consumers after devel/boost* update

With hat:	office
Sponsored by:	Future Crew, LLC
1.10.2_4
04 Jul 2024 11:39:44
commit hash: 149e2101c3c83b1cfdadcebfafb0208f1cf756b2commit hash: 149e2101c3c83b1cfdadcebfafb0208f1cf756b2commit hash: 149e2101c3c83b1cfdadcebfafb0208f1cf756b2commit hash: 149e2101c3c83b1cfdadcebfafb0208f1cf756b2 files touched by this commit		 Ganael LAPLANCHE (martymac) search for other commits by this committer 
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
commit hash: 96261a1e5aa94517a2203297c75c66f1269c075fcommit hash: 96261a1e5aa94517a2203297c75c66f1269c075fcommit hash: 96261a1e5aa94517a2203297c75c66f1269c075fcommit hash: 96261a1e5aa94517a2203297c75c66f1269c075f files touched by this commit		 Ganael LAPLANCHE (martymac) search for other commits by this committer 
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
commit hash: 0660187ad07f36727fead6764740a225a31f342fcommit hash: 0660187ad07f36727fead6764740a225a31f342fcommit hash: 0660187ad07f36727fead6764740a225a31f342fcommit hash: 0660187ad07f36727fead6764740a225a31f342f files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
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
commit hash: cf5d9b8b96202f197ff6ba7f254fb96bd8e578f0commit hash: cf5d9b8b96202f197ff6ba7f254fb96bd8e578f0commit hash: cf5d9b8b96202f197ff6ba7f254fb96bd8e578f0commit hash: cf5d9b8b96202f197ff6ba7f254fb96bd8e578f0 files touched by this commit		 Ganael LAPLANCHE (martymac) search for other commits by this committer 
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
commit hash: 22e222cbcea088a86fb58a5659742af50b337d86commit hash: 22e222cbcea088a86fb58a5659742af50b337d86commit hash: 22e222cbcea088a86fb58a5659742af50b337d86commit hash: 22e222cbcea088a86fb58a5659742af50b337d86 files touched by this commit		 Ganael LAPLANCHE (martymac) search for other commits by this committer 
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
commit hash: 24377618fdcc4ffcf2795b5a69236e494cd615b1commit hash: 24377618fdcc4ffcf2795b5a69236e494cd615b1commit hash: 24377618fdcc4ffcf2795b5a69236e494cd615b1commit hash: 24377618fdcc4ffcf2795b5a69236e494cd615b1 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/salmon: Set NOT_FOR_ARCHS to all 32-bit processors
1.10.2
21 Jul 2023 23:06:36
commit hash: 64a6421c248a048b13caab73de93ad10dd56e9cbcommit hash: 64a6421c248a048b13caab73de93ad10dd56e9cbcommit hash: 64a6421c248a048b13caab73de93ad10dd56e9cbcommit hash: 64a6421c248a048b13caab73de93ad10dd56e9cb files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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.

Number of commits found: 15
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