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Port details
pooler Optimise DNA sequencing primer-set combinations
1.89 biology on this many watch lists=2 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 1.88_1Version of this port present on the latest quarterly branch.
Maintainer: ssb22@cam.ac.uk search for ports maintained by this maintainer
Port Added: 2020-11-15 19:32:44
Last Update: 2025-02-01 01:36:31
Commit Hash: 70c1cdc
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
License: APACHE20
WWW:
https://ssb22.user.srcf.net/pooler/
Description:
Optimise combinations of primers and minimise the formation of dimers in multiplexed PCR. Primer Pooler can: * Check through each proposed pool for combinations that are likely to form dimers * Automatically move prospective amplicons between proposed pools to reduce dimer formation * Automatically search the genome sequence to find which amplicons overlap, and place their corresponding primers in separate pools * Optionally keep pool sizes within a specified range * Handle thousands of primers without being slow (useful for high-throughput sequencing applications) * Do all of the above with degenerate primers too.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (6 items)
Collapse this list.
  1. bin/pooler
  2. share/man/man1/pooler.1.gz
  3. share/applications/pooler.desktop
  4. /usr/local/share/licenses/pooler-1.89/catalog.mk
  5. /usr/local/share/licenses/pooler-1.89/LICENSE
  6. /usr/local/share/licenses/pooler-1.89/APACHE20
Collapse this list.
Dependency lines:
  • pooler>0:biology/pooler
To install the port:
cd /usr/ports/biology/pooler/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/pooler
  • pkg install pooler
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: pooler
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1738367688 SHA256 (ssb22-PrimerPooler-v1.89-gf33bf5d_GH0.tar.gz) = 8e4f91ee42191c4b3fd8d7036f75e067c66a76f1fd4d105231daf91a8e3e4976 SIZE (ssb22-PrimerPooler-v1.89-gf33bf5d_GH0.tar.gz) = 135036
Packages (timestamps in pop-ups are UTC):
pooler
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.891.89-1.891.89-1.76-
FreeBSD:13:quarterly1.88_11.88_1-1.88_11.88_11.881.881.88
FreeBSD:14:latest1.891.891.861.891.891.86-1.86
FreeBSD:14:quarterly1.88_11.88_1-1.88_11.88_11.881.881.88
FreeBSD:15:latest1.891.89n/a1.89n/a1.881.881.88_1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. update-desktop-database : devel/desktop-file-utils
Runtime dependencies:
  1. update-desktop-database : devel/desktop-file-utils
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_pooler
USES:
desktop-file-utils
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.89-gf33bf5d?dummy=/
Collapse this list.

Number of commits found: 18

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.89
01 Feb 2025 01:36:31
commit hash: 70c1cdc4a731a3772b61ddd5402f294867a16de6commit hash: 70c1cdc4a731a3772b61ddd5402f294867a16de6commit hash: 70c1cdc4a731a3772b61ddd5402f294867a16de6commit hash: 70c1cdc4a731a3772b61ddd5402f294867a16de6 files touched by this commit		 Wen Heping (wen) search for other commits by this committer 
biology/pooler: Update to 1.89

PR:		284463
Reported by:	ssb22@cam.ac.uk(maintainer)
1.88_1
22 Feb 2024 13:23:50
commit hash: 1b6126c582acbe774910efa441345a2c484495cbcommit hash: 1b6126c582acbe774910efa441345a2c484495cbcommit hash: 1b6126c582acbe774910efa441345a2c484495cbcommit hash: 1b6126c582acbe774910efa441345a2c484495cb files touched by this commit		 Muhammad Moinur Rahman (bofh) search for other commits by this committer 
biology/pooler: Moved man to share/man

Approved by:    portmgr (blanket)
1.88
10 Sep 2023 13:06:18
commit hash: 8abd028788bc719acea0697bb74f48894202e720commit hash: 8abd028788bc719acea0697bb74f48894202e720commit hash: 8abd028788bc719acea0697bb74f48894202e720commit hash: 8abd028788bc719acea0697bb74f48894202e720 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/pooler: Update to 1.88

Fix infinite loop

Changes: https://ssb22.user.srcf.net/pooler/#changes

PR:             273604
Reported by:    silas-freebsd@flatline.org.uk
1.86
19 Dec 2022 07:56:15
commit hash: a75fab4072ee1d5d0c5f8240986c016f123a97fdcommit hash: a75fab4072ee1d5d0c5f8240986c016f123a97fdcommit hash: a75fab4072ee1d5d0c5f8240986c016f123a97fdcommit hash: a75fab4072ee1d5d0c5f8240986c016f123a97fd files touched by this commit		 Fernando Apesteguía (fernape) search for other commits by this committer
Author: Silas S. Brown		 
biology/pooler: update to 1.86

ChangeLog:
https://github.com/ssb22/PrimerPooler/commit/0d2b55459d0689ad505a34fe54d2d7214890b13d

 * fix spurious memory error on M1 Mac

PR:		268445
Reported by:	silas-freebsd@flatline.org.uk (maintainer)
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.85
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.85
12 Jul 2022 12:47:45
commit hash: bcc206f2be0cca24bf8688ab6d81c351ccbc98d3commit hash: bcc206f2be0cca24bf8688ab6d81c351ccbc98d3commit hash: bcc206f2be0cca24bf8688ab6d81c351ccbc98d3commit hash: bcc206f2be0cca24bf8688ab6d81c351ccbc98d3 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/pooler: Update to 1.85

Change default annealing temperature from 37C to 45C

PR:             265163
Reported by:    silas-freebsd@flatline.org.uk
1.84
27 Apr 2022 13:22:12
commit hash: eaf43a218bf7781cf42e6d9924a7d0164f6ffec8commit hash: eaf43a218bf7781cf42e6d9924a7d0164f6ffec8commit hash: eaf43a218bf7781cf42e6d9924a7d0164f6ffec8commit hash: eaf43a218bf7781cf42e6d9924a7d0164f6ffec8 files touched by this commit		 Piotr Kubaj (pkubaj) search for other commits by this committer 
biology/pooler: use openmp only when omp.h is present
1.84
14 Mar 2022 14:41:38
commit hash: 3b861fa65fe8386404132158eb153378007483bfcommit hash: 3b861fa65fe8386404132158eb153378007483bfcommit hash: 3b861fa65fe8386404132158eb153378007483bfcommit hash: 3b861fa65fe8386404132158eb153378007483bf files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/pooler: Update to 1.84

Bug fix for high core-count machines

PR:             232454
Reported by:    silas-freebsd@flatline.org.uk
1.82
10 Feb 2022 14:23:48
commit hash: 8d34513c3f7ac851134d8452109c28497f0442cbcommit hash: 8d34513c3f7ac851134d8452109c28497f0442cbcommit hash: 8d34513c3f7ac851134d8452109c28497f0442cbcommit hash: 8d34513c3f7ac851134d8452109c28497f0442cb files touched by this commit		 Fernando Apesteguía (fernape) search for other commits by this committer 
biology/pooler: update to 1.82

ChangeLog: http://ssb22.user.srcf.net/pooler/#changes

PR:	261741
Reported by:	silas-freebsd@flatline.org.uk
1.78_1
06 Oct 2021 20:52:30
commit hash: 0716ab659929a0bd12bcff4faf0ab0993b297f14commit hash: 0716ab659929a0bd12bcff4faf0ab0993b297f14commit hash: 0716ab659929a0bd12bcff4faf0ab0993b297f14commit hash: 0716ab659929a0bd12bcff4faf0ab0993b297f14 files touched by this commit		 Piotr Kubaj (pkubaj) search for other commits by this committer 
biology/pooler: fix build on powerpc

In file included from bit-common.c:63:
In file included from ./bit-choice.h:23:
In file included from ./triangle.h:44:
./openmp.h:19:10: fatal error: 'omp.h' file not found
1.78_1
03 Oct 2021 17:47:27
commit hash: 07fb2d5e9d001934f1670d01aec1f536f14ebde2commit hash: 07fb2d5e9d001934f1670d01aec1f536f14ebde2commit hash: 07fb2d5e9d001934f1670d01aec1f536f14ebde2commit hash: 07fb2d5e9d001934f1670d01aec1f536f14ebde2 files touched by this commit		 Fernando Apesteguía (fernape) search for other commits by this committer 
*/*: Remove compiler:openmp from Mk/Uses/compiler.mk

The option implied a dependency on gcc but clang got openmp support long ago.

Remove compiler:openmp from Mk/Uses/compiler.mk

For ports using USE=compiler:openmp, just remove it and make them build with
clang.
Fix conditionals when necessary
Bump PORTREVISION where appropriate

If problem arises, they can be addressed by using USE_GCC=yes

An update to the Porter's Handbook will follow.

Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D31971
1.78
28 Aug 2021 14:35:01
commit hash: 541454f9939d3836bc1bcf642f8c748a1d04bb80commit hash: 541454f9939d3836bc1bcf642f8c748a1d04bb80commit hash: 541454f9939d3836bc1bcf642f8c748a1d04bb80commit hash: 541454f9939d3836bc1bcf642f8c748a1d04bb80 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/pooler: Update to 1.78

Adds desktop file

PR:             258120
Reported by:    Silas S. Brown <silas-freebsd@flatline.org.uk>
1.77
21 Aug 2021 22:12:35
commit hash: 472c25aa5d8dc3268fc5476b53100872d1900467commit hash: 472c25aa5d8dc3268fc5476b53100872d1900467commit hash: 472c25aa5d8dc3268fc5476b53100872d1900467commit hash: 472c25aa5d8dc3268fc5476b53100872d1900467 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/pooler: Update to 1.77

Minor fixes and enhancements.

Reported by:    silas-freebsd@flatline.org.uk
1.76
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
1.76
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
Remove # $FreeBSD$ from Makefiles.
1.76
08 Jan 2021 22:44:13
Revision:560817Original commit files touched by this commit		 jwb search for other commits by this committer 
biology/pooler: Upgrade to 1.76

Fixes race condition for make jobs in upstream Makefile

PR:             252352
Submitted by:   silas-freebsd@flatline.org.uk
1.75
15 Nov 2020 18:50:18
Revision:555418Original commit files touched by this commit		 jwb search for other commits by this committer 
biology/pooler: Optimise DNA sequencing primer-set combinations

Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.

Primer Pooler can:

* Check through each proposed pool for combinations that are likely to form
  dimers

* Automatically move prospective amplicons between proposed pools to reduce
  dimer formation

* Automatically search the genome sequence to find which amplicons overlap, and
  place their corresponding primers in separate pools
(Only the first 15 lines of the commit message are shown above View all of this commit message)

Number of commits found: 18
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