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Date:      Sun, 15 Nov 2020 18:50:18 +0000 (UTC)
From:      "Jason W. Bacon" <jwb@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r555418 - in head/biology: . pooler
Message-ID:  <202011151850.0AFIoICP055375@repo.freebsd.org>

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Author: jwb
Date: Sun Nov 15 18:50:17 2020
New Revision: 555418
URL: https://svnweb.freebsd.org/changeset/ports/555418

Log:
  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>

Added:
  head/biology/pooler/
  head/biology/pooler/Makefile   (contents, props changed)
  head/biology/pooler/distinfo   (contents, props changed)
  head/biology/pooler/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sun Nov 15 18:45:34 2020	(r555417)
+++ head/biology/Makefile	Sun Nov 15 18:50:17 2020	(r555418)
@@ -114,6 +114,7 @@
     SUBDIR += phyml
     SUBDIR += picard-tools
     SUBDIR += plink
+    SUBDIR += pooler
     SUBDIR += primer3
     SUBDIR += prodigal
     SUBDIR += prodigy-lig

Added: head/biology/pooler/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/pooler/Makefile	Sun Nov 15 18:50:17 2020	(r555418)
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=		pooler
+DISTVERSIONPREFIX=	v
+DISTVERSION=		1.75
+CATEGORIES=		biology
+
+MAINTAINER=	ssb22@cam.ac.uk
+COMMENT=	Optimise DNA sequencing primer-set combinations
+
+LICENSE=	APACHE20
+LICENSE_FILE=	${WRKDIR}/${GH_PROJECT}-${PORTVERSION}/LICENSE
+
+USES=		compiler:openmp
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	ssb22
+GH_PROJECT=	PrimerPooler
+
+WRKSRC_SUBDIR=	pooler
+CFLAGS+=	-fopenmp
+
+INSTALL_TARGET=	install-strip
+PLIST_FILES=	bin/pooler man/man1/pooler.1.gz
+
+.include <bsd.port.mk>

Added: head/biology/pooler/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/pooler/distinfo	Sun Nov 15 18:50:17 2020	(r555418)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1605447867
+SHA256 (ssb22-PrimerPooler-v1.75_GH0.tar.gz) = 7d0c0c6b58724a42100b1019995385568747f3b5620b09b297d3e77758c35818
+SIZE (ssb22-PrimerPooler-v1.75_GH0.tar.gz) = 125999

Added: head/biology/pooler/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/pooler/pkg-descr	Sun Nov 15 18:50:17 2020	(r555418)
@@ -0,0 +1,22 @@
+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/



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