diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2020-11-15 18:50:17 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2020-11-15 18:50:17 +0000 |
| commit | 018d7f39c9b4d74b52faa6df26b805b5d61e7002 (patch) | |
| tree | 7afffe915f08b699b48e8d7e9015706011602aa3 /biology/pooler | |
| parent | bf689b58be54f0891487378c04ee69b443c95ca1 (diff) | |
| download | ports-018d7f39c9b4d74b52faa6df26b805b5d61e7002.tar.gz ports-018d7f39c9b4d74b52faa6df26b805b5d61e7002.zip | |
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>
Notes
Notes:
svn path=/head/; revision=555418
Diffstat (limited to 'biology/pooler')
| -rw-r--r-- | biology/pooler/Makefile | 26 | ||||
| -rw-r--r-- | biology/pooler/distinfo | 3 | ||||
| -rw-r--r-- | biology/pooler/pkg-descr | 22 |
3 files changed, 51 insertions, 0 deletions
diff --git a/biology/pooler/Makefile b/biology/pooler/Makefile new file mode 100644 index 000000000000..6cb017752358 --- /dev/null +++ b/biology/pooler/Makefile @@ -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> diff --git a/biology/pooler/distinfo b/biology/pooler/distinfo new file mode 100644 index 000000000000..4423124ae190 --- /dev/null +++ b/biology/pooler/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1605447867 +SHA256 (ssb22-PrimerPooler-v1.75_GH0.tar.gz) = 7d0c0c6b58724a42100b1019995385568747f3b5620b09b297d3e77758c35818 +SIZE (ssb22-PrimerPooler-v1.75_GH0.tar.gz) = 125999 diff --git a/biology/pooler/pkg-descr b/biology/pooler/pkg-descr new file mode 100644 index 000000000000..3eb25cec500b --- /dev/null +++ b/biology/pooler/pkg-descr @@ -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/ |