pooler: Optimise DNA sequencing primer-set combinations

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Nov 15 19:22:49 2020 -0600
Changeset:	063cbece8f0346b2e817a09857721cf193d82399

Modified Files:
	Makefile
Added Files:
	pooler/DESCR
	pooler/Makefile
	pooler/PLIST
	pooler/distinfo
	pooler/patches/patch-Makefile

Log Message:
pooler: Optimise DNA sequencing primer-set combinations

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=063cbece8f0346b2e817a09857721cf193d82399

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                      |  1 +
 pooler/DESCR                  | 13 +++++++++++++
 pooler/Makefile               | 24 ++++++++++++++++++++++++
 pooler/PLIST                  |  3 +++
 pooler/distinfo               |  7 +++++++
 pooler/patches/patch-Makefile | 19 +++++++++++++++++++
 6 files changed, 67 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 69c1565958..729f7a6355 100644
--- a/Makefile
+++ b/Makefile
@@ -2962,6 +2962,7 @@ SUBDIR+=	polyclipping
 SUBDIR+=	polylib
 SUBDIR+=	polymul
 SUBDIR+=	ponyc
+SUBDIR+=	pooler
 SUBDIR+=	pop3.proxy
 SUBDIR+=	popup-el-current
 SUBDIR+=	portfwd
diff --git a/pooler/DESCR b/pooler/DESCR
new file mode 100644
index 0000000000..e69320eea1
--- /dev/null
+++ b/pooler/DESCR
@@ -0,0 +1,13 @@
+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.
diff --git a/pooler/Makefile b/pooler/Makefile
new file mode 100644
index 0000000000..f77f750f74
--- /dev/null
+++ b/pooler/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Sun Nov 15 19:12:26 CST 2020               #
+###########################################################
+
+DISTNAME=	pooler-1.75
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=ssb22/}
+GITHUB_PROJECT=	PrimerPooler
+GITHUB_TAG=	v1.75
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://ssb22.user.srcf.net/pooler/
+COMMENT=	Optimise DNA sequencing primer-set combinations
+LICENSE=	apache-2.0
+
+WRKSRC=		${WRKDIR}/${GITHUB_PROJECT}-1.75/pooler
+CFLAGS+=	-fopenmp
+
+INSTALL_TARGET=		install-strip
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/pooler/PLIST b/pooler/PLIST
new file mode 100644
index 0000000000..cea213faf3
--- /dev/null
+++ b/pooler/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/pooler
+man/man1/pooler.1
diff --git a/pooler/distinfo b/pooler/distinfo
new file mode 100644
index 0000000000..2fc79998be
--- /dev/null
+++ b/pooler/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (pooler-1.75.tar.gz) = 1b8c92087d40c664dc6547b58cccaa966d7273a2
+RMD160 (pooler-1.75.tar.gz) = 2f0a7b2388fb20c18e231c3b3f917762f58b2d54
+SHA512 (pooler-1.75.tar.gz) = d72f063455aaf5eb9de30cbbfd649cc069af4192d2f2aaf4d20d5f70973a41a0e92f660842e306d557ab8737de0d95ce0021cfbd247251b2f0f3e255ca13b487
+Size (pooler-1.75.tar.gz) = 125999 bytes
+SHA1 (patch-Makefile) = 97f8c8a673564311be5ff4134eda83dd095252db
diff --git a/pooler/patches/patch-Makefile b/pooler/patches/patch-Makefile
new file mode 100644
index 0000000000..7e91ecd040
--- /dev/null
+++ b/pooler/patches/patch-Makefile
@@ -0,0 +1,19 @@
+$NetBSD$
+
+# Create install dirs
+
+--- Makefile.orig	2020-11-16 01:19:09.379126643 +0000
++++ Makefile
+@@ -130,6 +130,7 @@ publish-src: test-other
+ # compatibility with bsd.port.mk:
+ all: pooler
+ install: all
++	$(MKDIR) -p $(DESTDIR)/$(PREFIX)/bin $(DESTDIR)/$(PREFIX)/man/man1
+ 	$(INSTALL_PROGRAM) pooler $(DESTDIR)/$(PREFIX)/bin/
+ 	$(INSTALL_MAN) pooler.1 $(DESTDIR)/$(PREFIX)/man/man1/
+ install-strip: install
+@@ -138,3 +139,4 @@ PREFIX          ?= usr/local
+ INSTALL_PROGRAM ?= cp
+ INSTALL_MAN     ?= cp
+ STRIP           ?= strip
++MKDIR		?= mkdir