'Add dazz_db: Dresden assembler for long read DNA projects'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 11:27:23 2017 -0500
Changeset:	b54e9cab690e4918250a196c8a63a056ef3295e2

Modified Files:
	Makefile
Added Files:
	dazz_db/DESCR
	dazz_db/Makefile
	dazz_db/PLIST
	dazz_db/TODO
	dazz_db/buildlink3.mk
	dazz_db/distinfo

Log Message:
'Add dazz_db: 	Dresden assembler for long read DNA projects'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=b54e9cab690e4918250a196c8a63a056ef3295e2

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

diffstat:
 Makefile              |  1 +
 dazz_db/DESCR         |  3 +++
 dazz_db/Makefile      | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++
 dazz_db/PLIST         | 17 +++++++++++++++
 dazz_db/TODO          |  1 +
 dazz_db/buildlink3.mk | 12 +++++++++++
 dazz_db/distinfo      |  6 ++++++
 7 files changed, 100 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 1cdef89dd0..12f5404fbb 100644
--- a/Makefile
+++ b/Makefile
@@ -469,6 +469,7 @@ SUBDIR+=	datamash
 SUBDIR+=	datapipe
 SUBDIR+=	dates
 SUBDIR+=	davical-git
+SUBDIR+=	dazz_db
 SUBDIR+=	db1
 SUBDIR+=	dbf
 SUBDIR+=	dbus-dfbsd
diff --git a/dazz_db/DESCR b/dazz_db/DESCR
new file mode 100644
index 0000000000..c86c5a0f6a
--- /dev/null
+++ b/dazz_db/DESCR
@@ -0,0 +1,3 @@
+The Dazzler Data Base.
+
+WWW: https://github.com/thegenemyers/DAZZ_DB
diff --git a/dazz_db/Makefile b/dazz_db/Makefile
new file mode 100644
index 0000000000..f3fa5b8ff5
--- /dev/null
+++ b/dazz_db/Makefile
@@ -0,0 +1,60 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+# Must use the same version of dazz_db, daligner, pypeflow, and falcon!
+
+DISTNAME=	dazz_db-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://acadix.biz/Ports/distfiles/
+EXTRACT_SUFX=	.tar.xz
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	Dresden assembler for long read DNA projects
+# Double-check this
+LICENSE=	modified-bsd
+
+# Pessimistic assumption.  Test and change if possible.
+# MAKE_JOBS_SAFE=	no
+
+USE_LANGUAGES=	c
+USE_TOOLS+=	gmake
+MAKE_FILE=	GNUmakefile
+
+# OS X Snow Leopard doesn't suppot no-unused-result and dies of an
+# internal compiler error if we use -O2 or higher
+SUBST_CLASSES+=		makefile
+SUBST_STAGE.makefile=	post-patch
+SUBST_FILES.makefile=	${WRKSRC}/GNUmakefile
+SUBST_SED.makefile=	-e 's|-Wno-unused-result||g' \
+			-e 's|-O3|-O|g'
+
+PORTVERSION=	2015.10.28
+
+AUTO_MKDIRS=	yes
+
+do-install:
+	${INSTALL_PROGRAM} \
+		${WRKSRC}/Catrack \
+		${WRKSRC}/DAM2fasta \
+		${WRKSRC}/DB2fasta \
+		${WRKSRC}/DB2quiva \
+		${WRKSRC}/DBdust \
+		${WRKSRC}/DBrm \
+		${WRKSRC}/DBshow \
+		${WRKSRC}/DBsplit \
+		${WRKSRC}/DBstats \
+		${WRKSRC}/fasta2DAM \
+		${WRKSRC}/fasta2DB \
+		${WRKSRC}/quiva2DB \
+		${WRKSRC}/simulator \
+		${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} \
+		${WRKSRC}/*.h ${DESTDIR}${PREFIX}/include
+	${INSTALL_DATA} \
+		${WRKSRC}/libdazzdb.a ${DESTDIR}${PREFIX}/lib
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/dazz_db/PLIST b/dazz_db/PLIST
new file mode 100644
index 0000000000..890a485d77
--- /dev/null
+++ b/dazz_db/PLIST
@@ -0,0 +1,17 @@
+@comment $NetBSD$
+bin/Catrack
+bin/DAM2fasta
+bin/DB2fasta
+bin/DB2quiva
+bin/DBdust
+bin/DBrm
+bin/DBshow
+bin/DBsplit
+bin/DBstats
+bin/fasta2DAM
+bin/fasta2DB
+bin/quiva2DB
+bin/simulator
+include/DB.h
+include/QV.h
+lib/libdazzdb.a
diff --git a/dazz_db/TODO b/dazz_db/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/dazz_db/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/dazz_db/buildlink3.mk b/dazz_db/buildlink3.mk
new file mode 100644
index 0000000000..88c09a6a0d
--- /dev/null
+++ b/dazz_db/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	dazz_db
+
+.if !defined(DAZZ_DB_BUILDLINK3_MK)
+DAZZ_DB_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.dazz_db+=	dazz_db>=2015.08.17
+BUILDLINK_PKGSRCDIR.dazz_db?=	../../wip/dazz_db
+.endif	# DAZZ_DB_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-dazz_db
diff --git a/dazz_db/distinfo b/dazz_db/distinfo
new file mode 100644
index 0000000000..6520e42afc
--- /dev/null
+++ b/dazz_db/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (dazz_db-2015.10.28.tar.xz) = 6afa5d9e44a230923214bf19db4f0e774d00146d
+RMD160 (dazz_db-2015.10.28.tar.xz) = a3324f7e13ad7069ff2214afdf1e1fb94a1802e6
+SHA512 (dazz_db-2015.10.28.tar.xz) = 9262a5e3259b99ff70fe56111be708963e1b9e25af62c1d3289a7abc6d825ce957949d1b90db441ac9057a37665fbc4017ccef0f1fe78f27877b3c92a25e2f68
+Size (dazz_db-2015.10.28.tar.xz) = 49300 bytes