biology/pooler 1.89

biology/pooler: Update to 1.89

PR:		284463
Reported by:	ssb22@cam.ac.uk(maintainer)

biology/pooler: Moved man to share/man

Approved by:    portmgr (blanket)

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

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)

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)

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.

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 1.85

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 present

biology/pooler: Update to 1.84

Bug fix for high core-count machines

PR:             232454
Reported by:    silas-freebsd@flatline.org.uk

biology/pooler: update to 1.82

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

PR:	261741
Reported by:	silas-freebsd@flatline.org.uk

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

*/*: 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

biology/pooler: Update to 1.78

Adds desktop file

PR:             258120
Reported by:    Silas S. Brown <silas-freebsd@flatline.org.uk>

biology/pooler: Update to 1.77

Minor fixes and enhancements.

Reported by:    silas-freebsd@flatline.org.uk

One more small cleanup, forgotten yesterday. Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/pooler: Upgrade to 1.76

Fixes race condition for make jobs in upstream Makefile

PR:             252352
Submitted by:   silas-freebsd@flatline.org.uk

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

* 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>