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Bacon" Date: Sun, 15 Nov 2020 18:50:18 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r555418 - in head/biology: . pooler X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . pooler X-SVN-Commit-Revision: 555418 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 15 Nov 2020 18:50:19 -0000 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 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 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/