notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)Want a good monitor light? See my photosAll times are UTC		 Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
salmon Transcript-level quantification of RNA-seq from lightweight alignments
1.10.2_3 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_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: 2024-04-17 11:28:34
Commit Hash: 96261a1
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_3/catalog.mk
  3. /usr/local/share/licenses/salmon-1.10.2_3/LICENSE
  4. /usr/local/share/licenses/salmon-1.10.2_3/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

Collapse this list.

Packages (timestamps in pop-ups are UTC):
salmon
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.10.2_21.10.2_3------
FreeBSD:13:quarterly1.10.2_21.10.2_2------
FreeBSD:14:latest1.10.2_21.10.2_3------
FreeBSD:14:quarterly1.10.2_21.10.2_2------
FreeBSD:15:latest1.10.2_31.10.2_3n/a-n/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. cmake : devel/cmake-core
  8. gmake>=4.4.1 : 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: 6

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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: 6
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
Security Policy
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
glpiApr 28
py-social-auth-app-djangoApr 28
chromiumApr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25
glpi*Apr 25

36 vulnerabilities affecting 208 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last processed:
2024-04-29 10:45:39 UTC


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)

Calculated hourly:
Port count 32206
Broken 81
Deprecated 157
Ignore 212
Forbidden 2
Restricted 2
No CDROM 1
Vulnerable 37
Expired 13
Set to expire 130
Interactive 0
new 24 hours 2
new 48 hours5
new 7 days19
new fortnight35
new month100
Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD 		Valid HTML, CSS, and RSS. Copyright © 2000-2024 Dan Langille. All rights reserved.