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Port details
pooler Optimise DNA sequencing primer-set combinations
1.85 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 Version 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: 2022-07-12 12:47:45
Commit Hash: bcc206f
License: APACHE20
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (6 items)
Collapse this list.
  1. bin/pooler
  2. man/man1/pooler.1.gz
  3. share/applications/pooler.desktop
  4. /usr/local/share/licenses/pooler-1.85/catalog.mk
  5. /usr/local/share/licenses/pooler-1.85/LICENSE
  6. /usr/local/share/licenses/pooler-1.85/APACHE20
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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:
Packages (timestamps in pop-ups are UTC):
pooler
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd641.781.76
FreeBSD:11:armv6--
FreeBSD:11:i3861.781.76
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-1.84
FreeBSD:12:amd641.851.84
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3861.851.84
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-1.76
FreeBSD:13:aarch641.851.84
FreeBSD:13:amd641.851.84
FreeBSD:13:armv6-1.84
FreeBSD:13:armv71.851.84
FreeBSD:13:i3861.851.84
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc641.761.76
FreeBSD:13:riscv64-1.84
FreeBSD:14:aarch641.85-
FreeBSD:14:amd641.85-
FreeBSD:14:armv61.85-
FreeBSD:14:armv71.85-
FreeBSD:14:i3861.85-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc641.76-
FreeBSD:14:riscv641.78_1-
 

There are no ports dependent upon this port

Configuration Options:
Options name:
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/v1.85?dummy=/
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Number of commits found: 12

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Jul 2022 12:47:45
 files touched by this commit commit hash:bcc206f2be0cca24bf8688ab6d81c351ccbc98d3  1.85
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
27 Apr 2022 13:22:12
 files touched by this commit commit hash:eaf43a218bf7781cf42e6d9924a7d0164f6ffec8  1.84
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/pooler: use openmp only when omp.h is present
14 Mar 2022 14:41:38
 files touched by this commit commit hash:3b861fa65fe8386404132158eb153378007483bf  1.84
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
10 Feb 2022 14:23:48
 files touched by this commit commit hash:8d34513c3f7ac851134d8452109c28497f0442cb  1.82
Fernando ApesteguĂ­a (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
06 Oct 2021 20:52:30
 files touched by this commit commit hash:0716ab659929a0bd12bcff4faf0ab0993b297f14  1.78_1
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
03 Oct 2021 17:47:27
 files touched by this commit commit hash:07fb2d5e9d001934f1670d01aec1f536f14ebde2  1.78_1
Fernando ApesteguĂ­a (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
28 Aug 2021 14:35:01
 files touched by this commit commit hash:541454f9939d3836bc1bcf642f8c748a1d04bb80  1.78
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>
21 Aug 2021 22:12:35
 files touched by this commit commit hash:472c25aa5d8dc3268fc5476b53100872d1900467  1.77
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
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  1.76
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.76
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
08 Jan 2021 22:44:13
Original commit files touched by this commit Revision:560817  1.76
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
15 Nov 2020 18:50:18
Original commit files touched by this commit Revision:555418  1.75
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: 12