'Add daligner: Find all significant local alignments between reads'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 11:46:37 2017 -0500
Changeset:	f8278fa35f5ba0923299e992a1f7e8a823b02213

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

Log Message:
'Add daligner: 	Find all significant local alignments between reads'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f8278fa35f5ba0923299e992a1f7e8a823b02213

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

diffstat:
 Makefile               |  1 +
 daligner/DESCR         |  3 ++
 daligner/Makefile      | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++
 daligner/PLIST         | 21 ++++++++++++++
 daligner/TODO          |  1 +
 daligner/buildlink3.mk | 12 ++++++++
 daligner/distinfo      |  6 ++++
 7 files changed, 118 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 12f5404fbb..b81f87b667 100644
--- a/Makefile
+++ b/Makefile
@@ -458,6 +458,7 @@ SUBDIR+=	d-feet
 SUBDIR+=	d1x-rebirth
 SUBDIR+=	d2x-rebirth
 SUBDIR+=	d4x
+SUBDIR+=	daligner
 SUBDIR+=	daphne
 SUBDIR+=	daq
 SUBDIR+=	darcnes-svgalib
diff --git a/daligner/DESCR b/daligner/DESCR
new file mode 100644
index 0000000000..9b0ea503eb
--- /dev/null
+++ b/daligner/DESCR
@@ -0,0 +1,3 @@
+Find all significant local alignments between reads.
+
+WWW: https://github.com/thegenemyers/DALIGNER
diff --git a/daligner/Makefile b/daligner/Makefile
new file mode 100644
index 0000000000..06ff528a57
--- /dev/null
+++ b/daligner/Makefile
@@ -0,0 +1,74 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+## Must use the same version of dazz_db, daligner, pypeflow, and falcon!
+
+DISTNAME=	daligner-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://acadix.biz/Ports/distfiles/
+EXTRACT_SUFX=	.tar.xz
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	Find all significant local alignments between reads
+# Double-check this
+LICENSE=	modified-bsd
+
+# Pessimistic assumption.  Test and change if possible.
+# MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c
+USE_TOOLS+=	gmake
+
+# 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=	${WRKSRC}/GNUmakefile
+SUBST_SED.makefile=	-e 's|-Wno-unused-result||g'
+SUBST_SED.makefile+=	-e 's|-O3|-O|g'
+
+CFLAGS+=	-I${PREFIX}/include
+MAKE_FILE=	GNUmakefile
+
+PORTVERSION=	2015.10.28
+
+AUTO_MKDIRS=	yes
+
+post-patch:
+	for f in ${WRKSRC}/py_utils/*.py; do \
+		${PRINTF} "#!${PYTHONBIN}\\n" > $$f.temp; \
+		${CAT} $$f >> $$f.temp; \
+		${MV} -f $$f.temp $$f; \
+	done
+
+do-install:
+	${INSTALL_PROGRAM} \
+		${WRKSRC}/DB2Falcon \
+		${WRKSRC}/HPCdaligner \
+		${WRKSRC}/HPCmapper \
+		${WRKSRC}/LA4Falcon \
+		${WRKSRC}/LAcat \
+		${WRKSRC}/LAcheck \
+		${WRKSRC}/LAmerge \
+		${WRKSRC}/LAshow \
+		${WRKSRC}/LAsort \
+		${WRKSRC}/LAsplit \
+		${WRKSRC}/daligner \
+		${WRKSRC}/daligner_p \
+		${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} \
+		${WRKSRC}/py_utils/*.py \
+		${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} \
+		${WRKSRC}/*.h \
+		${DESTDIR}${PREFIX}/include
+	${AR} rs ${DESTDIR}${PREFIX}/lib/libdaligner.a \
+		${WRKSRC}/align.o
+
+.include "../../wip/dazz_db/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/daligner/PLIST b/daligner/PLIST
new file mode 100644
index 0000000000..8150b5071f
--- /dev/null
+++ b/daligner/PLIST
@@ -0,0 +1,21 @@
+@comment $NetBSD$
+bin/daligner
+bin/daligner_p
+bin/DAPipe.py
+bin/DAPI.py
+bin/DB2Falcon
+bin/DBLA_to_falcon.py
+bin/HPCdaligner
+bin/HPCmapper
+bin/LA4Falcon
+bin/LAcat
+bin/LAcheck
+bin/LAmerge
+bin/LAPipe.py
+bin/LAPI.py
+bin/LAshow
+bin/LAsort
+bin/LAsplit
+include/align.h
+include/filter.h
+lib/libdaligner.a
diff --git a/daligner/TODO b/daligner/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/daligner/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/daligner/buildlink3.mk b/daligner/buildlink3.mk
new file mode 100644
index 0000000000..4d8a9da088
--- /dev/null
+++ b/daligner/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	daligner
+
+.if !defined(DALIGNER_BUILDLINK3_MK)
+DALIGNER_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.daligner+=	daligner-2015.10.28{,nb*}
+BUILDLINK_PKGSRCDIR.daligner?=	../../wip/daligner
+.endif	# DALIGNER_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-daligner
diff --git a/daligner/distinfo b/daligner/distinfo
new file mode 100644
index 0000000000..fa9174ec8d
--- /dev/null
+++ b/daligner/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (daligner-2015.10.28.tar.xz) = b11d0e62f2e14a2bf10c51d2118fc9b1ae5925ea
+RMD160 (daligner-2015.10.28.tar.xz) = 813725f49fb82431b7c0397874732bc5368c84c6
+SHA512 (daligner-2015.10.28.tar.xz) = 39e3e760b378711df043223805670ee256ac7f0a8c29d74bc103ffd09844fa09fdfb02925c76ce841fa5c3b51f53f385f3edb66fafed824411f7cc60f3655579
+Size (daligner-2015.10.28.tar.xz) = 57128 bytes