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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_2Version 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: 2026-05-07 21:47:29
Commit Hash: 2a7c056
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 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_21.10.3_2---n/an/an/a
FreeBSD:14:latest1.10.3_21.10.3_2------
FreeBSD:14:quarterly1.10.3_21.10.3_2------
FreeBSD:15:latest1.10.3_21.10.3_2n/a-n/an/a--
FreeBSD:15:quarterly1.10.3_21.10.3_2n/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: 16

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.10.3_2
07 May 2026 21:47:29
commit hash: 2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4acommit hash: 2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4acommit hash: 2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4acommit hash: 2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4a files touched by this commit		 Rene Ladan (rene) search for other commits by this committer 
all: drop support for FreeBSD 13, mips and risc64sf

Reviewed by:            many (*)
Differential Revision:  https://reviews.freebsd.org/D55624
Differential Revision:  https://reviews.freebsd.org/D55642 (merged in from bofh)

many (*)
  acm arrowd brooks cmt dch decke dinoex eduardo fluffy fuz gahr garga
  jbeich joerg jrm kai kenrap martymac matthew mfechner michaelo mizhka
  nobutaka pkubaj se tagattie thj

  Anton Saietskii
  GenericRikka
  Gert Doering
  Jan Bramkamp
  Oleh Hushchenkov
  Oleksandr Kryvulia
  Ralf van der Enden
  Yamagi

  desktop kde python tcltk office
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: 16
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