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* biology/pooler: Update to 1.89Wen Heping2025-02-011-3/+3
| | | | | PR: 284463 Reported by: ssb22@cam.ac.uk(maintainer)
* biology/pooler: Moved man to share/manMuhammad Moinur Rahman2024-02-221-1/+5
| | | | Approved by: portmgr (blanket)
* biology/pooler: Update to 1.88Jason W. Bacon2023-09-101-1/+1
| | | | | | | | | Fix infinite loop Changes: https://ssb22.user.srcf.net/pooler/#changes PR: 273604 Reported by: silas-freebsd@flatline.org.uk
* biology/pooler: update to 1.86Silas S. Brown2022-12-191-1/+2
| | | | | | | | | 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)
* Add WWW entries to port MakefilesStefan Eßer2022-09-071-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner)
* biology/pooler: Update to 1.85Jason W. Bacon2022-07-121-1/+1
| | | | | | | Change default annealing temperature from 37C to 45C PR: 265163 Reported by: silas-freebsd@flatline.org.uk
* biology/pooler: use openmp only when omp.h is presentPiotr Kubaj2022-04-271-5/+2
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* biology/pooler: Update to 1.84Jason W. Bacon2022-03-141-1/+1
| | | | | | | Bug fix for high core-count machines PR: 232454 Reported by: silas-freebsd@flatline.org.uk
* biology/pooler: update to 1.82Fernando Apesteguía2022-02-101-4/+3
| | | | | | | ChangeLog: http://ssb22.user.srcf.net/pooler/#changes PR: 261741 Reported by: silas-freebsd@flatline.org.uk
* biology/pooler: fix build on powerpcPiotr Kubaj2021-10-061-1/+6
| | | | | | | 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
* */*: Remove compiler:openmp from Mk/Uses/compiler.mkFernando Apesteguía2021-10-031-3/+2
| | | | | | | | | | | | | | | | | | 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
* biology/pooler: Update to 1.78Jason W. Bacon2021-08-281-2/+2
| | | | | | | Adds desktop file PR: 258120 Reported by: Silas S. Brown <silas-freebsd@flatline.org.uk>
* biology/pooler: Update to 1.77Jason W. Bacon2021-08-211-1/+3
| | | | | | Minor fixes and enhancements. Reported by: silas-freebsd@flatline.org.uk
* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/pooler: Upgrade to 1.76Jason W. Bacon2021-01-081-1/+1
| | | | | | | | | | Fixes race condition for make jobs in upstream Makefile PR: 252352 Submitted by: silas-freebsd@flatline.org.uk Notes: svn path=/head/; revision=560817
* biology/pooler: Optimise DNA sequencing primer-set combinationsJason W. Bacon2020-11-151-0/+26
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/ PR: ports/251065 Submitted by: Silas S. Brown <silas-freebsd@flatline.org.uk> Notes: svn path=/head/; revision=555418
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