svn commit: r555418 - in head/biology: . pooler
Jason W. Bacon
jwb at FreeBSD.org
Sun Nov 15 18:50:19 UTC 2020
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 at 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 at 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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