| Port details |
- pooler Optimise DNA sequencing primer-set combinations
- 1.85 biology
 =0      Version of this port present on the latest quarterly branch. - Maintainer: ssb22@cam.ac.uk
- Port Added: 2020-11-15 19:32:44
- Last Update: 2022-07-12 12:47:45
- Commit Hash: bcc206f
- License: APACHE20
- 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.
WWW: http://ssb22.user.srcf.net/pooler/
- SVNWeb : git : Homepage
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- 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 = 1657629092
SHA256 (ssb22-PrimerPooler-v1.85_GH0.tar.gz) = f26e7143b1bb837693bb894ee6b6276b2a89b8b9b7502a847df1e46d4fc5a83a
SIZE (ssb22-PrimerPooler-v1.85_GH0.tar.gz) = 130270
- Packages (timestamps in pop-ups are UTC):
- There are no ports dependent upon this port
- Configuration Options:
- No options to configure
- Options name:
- biology_pooler
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: see SVNWeb link above for full details) |
| Date | By | Description |
|---|
12 Jul 2022 12:47:45
  1.85 |
Jason W. Bacon (jwb) |
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
1.84 |
Piotr Kubaj (pkubaj) |
biology/pooler: use openmp only when omp.h is present |
14 Mar 2022 14:41:38
1.84 |
Jason W. Bacon (jwb) |
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
1.82 |
Fernando Apesteguía (fernape) |
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
1.78_1 |
Piotr Kubaj (pkubaj) |
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
1.78_1 |
Fernando Apesteguía (fernape) |
*/*: 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
1.78 |
Jason W. Bacon (jwb) |
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
1.77 |
Jason W. Bacon (jwb) |
biology/pooler: Update to 1.77
Minor fixes and enhancements.
Reported by: silas-freebsd@flatline.org.uk |
07 Apr 2021 08:09:01
1.76 |
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
06 Apr 2021 14:31:07
1.76 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
08 Jan 2021 22:44:13
  1.76 |
jwb |
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
1.75 |
jwb |
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  ) |
As an Amazon Associate I earn from qualifying purchases.