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Port details
salmon Transcript-level quantification of RNA-seq from lightweight alignments
1.10.2_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 1.10.2_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: 2023-11-28 11:35:02
Commit Hash: cf5d9b8
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-1.10.2_2/catalog.mk
  3. /usr/local/share/licenses/salmon-1.10.2_2/LICENSE
  4. /usr/local/share/licenses/salmon-1.10.2_2/GPLv3
Collapse this list.
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 = 1689958260 SHA256 (COMBINE-lab-salmon-v1.10.2_GH0.tar.gz) = 976989182160fef3afb4429ee8b85d8dd39ed6ca212bb14d6a65cde0e985fb98 SIZE (COMBINE-lab-salmon-v1.10.2_GH0.tar.gz) = 7193261

Expand this list (6 items)

Collapse this list.

SHA256 (COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz) = b90ce8079c375136d12e37bc23e451ae34a49d49c54f6cdd2050ba8add758ab4 SIZE (COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz) = 3368053 SHA256 (jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz) = 4444c78846e49a493ff09d56d55ebe61140bb0a76ec5fa1c27eff13ec9dabd8b SIZE (jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz) = 3382074 SHA256 (samtools-htscodecs-5aecc6e_GH0.tar.gz) = 3abb6a8516761bf0db5149c3d6c077e2d540470180245c2afb1f4400158b1f54 SIZE (samtools-htscodecs-5aecc6e_GH0.tar.gz) = 3191442

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Packages (timestamps in pop-ups are UTC):
salmon
ABIlatestquarterly
FreeBSD:12:aarch64-1.10.2_1
FreeBSD:12:amd641.10.2_11.10.2_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch641.10.2_11.10.2_1
FreeBSD:13:amd641.10.2_11.10.2_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:13:riscv64--
FreeBSD:14:aarch641.10.2_11.10.2_1
FreeBSD:14:amd641.10.2_11.10.2_1
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
FreeBSD:14:riscv64--
FreeBSD:15:amd641.10.2_2-
FreeBSD:15:armv6--
FreeBSD:15:armv7--
FreeBSD:15:i386--
FreeBSD:15:mips64--
FreeBSD:15:powerpc64--
FreeBSD:15:riscv64--
 
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. cmake : devel/cmake-core
  8. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libboost_system.so : devel/boost-libs
  2. libtbb.so : devel/onetbb
  3. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/
Collapse this list.

Number of commits found: 4

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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: 4
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