'Add cdbfasta: Fast indexing and retrieval of fasta records from flat file databases'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 12:05:12 2017 -0500
Changeset:	378948b5cfb8d6319f40f5c9183d5ade8303b144

Modified Files:
	Makefile
Added Files:
	cdbfasta/DESCR
	cdbfasta/Makefile
	cdbfasta/PLIST
	cdbfasta/TODO
	cdbfasta/buildlink3.mk
	cdbfasta/distinfo
	cdbfasta/patches/patch-Makefile

Log Message:
'Add cdbfasta: 	Fast indexing and retrieval of fasta records from flat file databases'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=378948b5cfb8d6319f40f5c9183d5ade8303b144

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

diffstat:
 Makefile                        |  1 +
 cdbfasta/DESCR                  |  3 ++
 cdbfasta/Makefile               | 33 ++++++++++++++++++++++
 cdbfasta/PLIST                  |  3 ++
 cdbfasta/TODO                   |  1 +
 cdbfasta/buildlink3.mk          | 12 ++++++++
 cdbfasta/distinfo               |  7 +++++
 cdbfasta/patches/patch-Makefile | 61 +++++++++++++++++++++++++++++++++++++++++
 8 files changed, 121 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 0395724362..8853104900 100644
--- a/Makefile
+++ b/Makefile
@@ -310,6 +310,7 @@ SUBDIR+=	cataclysm-dda
 SUBDIR+=	cb2bib
 SUBDIR+=	ccnet-server
 SUBDIR+=	ccrypt
+SUBDIR+=	cdbfasta
 SUBDIR+=	cddlib
 SUBDIR+=	cde
 SUBDIR+=	cdirip
diff --git a/cdbfasta/DESCR b/cdbfasta/DESCR
new file mode 100644
index 0000000000..9676c40a92
--- /dev/null
+++ b/cdbfasta/DESCR
@@ -0,0 +1,3 @@
+Fast indexing and retrieval of fasta records from flat file data bases.
+
+WWW: http://sourceforge.net/projects/cdbfasta/
diff --git a/cdbfasta/Makefile b/cdbfasta/Makefile
new file mode 100644
index 0000000000..4fe5e56bab
--- /dev/null
+++ b/cdbfasta/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	cdbfasta-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://acadix.biz/Ports/distfiles/
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	Fast indexing and retrieval of fasta records from flat file databases
+# LICENSE=	Unspecified
+
+# Pessimistic assumption.  Test and change if possible.
+MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+
+WRKSRC=		${WRKDIR}/cdbfasta
+
+PORTVERSION=	2010.07.22
+
+AUTO_MKDIRS=	yes
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/cdbfasta ${DESTDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/cdbyank ${DESTDIR}${PREFIX}/bin
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/cdbfasta/PLIST b/cdbfasta/PLIST
new file mode 100644
index 0000000000..66edc1ab05
--- /dev/null
+++ b/cdbfasta/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/cdbfasta
+bin/cdbyank
diff --git a/cdbfasta/TODO b/cdbfasta/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/cdbfasta/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/cdbfasta/buildlink3.mk b/cdbfasta/buildlink3.mk
new file mode 100644
index 0000000000..b8dce7e9ed
--- /dev/null
+++ b/cdbfasta/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	cdbfasta
+
+.if !defined(CDBFASTA_BUILDLINK3_MK)
+CDBFASTA_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.cdbfasta+=	cdbfasta>=2010.07.22
+BUILDLINK_PKGSRCDIR.cdbfasta?=	../../wip/cdbfasta
+.endif	# CDBFASTA_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-cdbfasta
diff --git a/cdbfasta/distinfo b/cdbfasta/distinfo
new file mode 100644
index 0000000000..185ecae269
--- /dev/null
+++ b/cdbfasta/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (cdbfasta-2010.07.22.tar.gz) = 2419421ab1d753d3bb8778c92236da74fee30526
+RMD160 (cdbfasta-2010.07.22.tar.gz) = c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a
+SHA512 (cdbfasta-2010.07.22.tar.gz) = 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e
+Size (cdbfasta-2010.07.22.tar.gz) = 59735 bytes
+SHA1 (patch-Makefile) = 9ac728af0e7f1149ab1ae226759591df2e34096e
diff --git a/cdbfasta/patches/patch-Makefile b/cdbfasta/patches/patch-Makefile
new file mode 100644
index 0000000000..5df71c6fe4
--- /dev/null
+++ b/cdbfasta/patches/patch-Makefile
@@ -0,0 +1,61 @@
+$NetBSD$
+
+--- Makefile.orig	2015-02-18 10:08:59.000000000 -0600
++++ Makefile	2015-02-18 10:41:31.000000000 -0600
+@@ -18,7 +18,9 @@
+     MARCH = 
+ endif    
+ 
+-CC      := g++
++# Use the correct compiler (CXX, not CC) and respect the environment
+++CXX?=g++
++
+ BASEFLAGS  = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 \
+ -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \
+ -D_REENTRANT 
+@@ -33,25 +35,25 @@
+ endif
+ 
+ ifeq ($(findstring nommap,$(MAKECMDGOALS)),)
+-  CFLAGS = $(DBGFLAGS) $(BASEFLAGS)
++  CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS)
+ else
+-  CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
++  CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
+ endif
+ 
+ %.o : %.c
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.cc
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.C
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.cpp
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.cxx
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ # C/C++ linker
+ 
+@@ -65,10 +67,10 @@
+ debug:  all
+ nommap: all
+ cdbfasta:  ./cdbfasta.o ./gcdbz.o $(LIBS) ${GCLDIR}/gcdb.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
+-	${LINKER} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
++	${CXX} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
+ 
+ cdbyank :  ./cdbyank.o ./gcdbz.o ${GCLDIR}/gcdb.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
+-	${LINKER} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
++	${CXX} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
+ 
+ # target for removing all object files
+