diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/pooler/Makefile | 26 | ||||
| -rw-r--r-- | biology/pooler/distinfo | 3 | ||||
| -rw-r--r-- | biology/pooler/pkg-descr | 22 |
4 files changed, 52 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 29616c908fff..18a5394e98b0 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -114,6 +114,7 @@ SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink + SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig 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/ |