biology/fastahack: Utility for indexing and sequence extraction from FASTA files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15080

biology/Makefile

@@ -26,6 +26,7 @@
     SUBDIR += emboss
     SUBDIR += fasta
     SUBDIR += fasta3
+    SUBDIR += fastahack
     SUBDIR += fastdnaml
     SUBDIR += fastool
     SUBDIR += fastqc

biology/fastahack/Makefile

@@ -0,0 +1,19 @@
+# $FreeBSD$
+
+PORTNAME=	fastahack
+DISTVERSION=	g20160702
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Utility for indexing and sequence extraction from FASTA files
+
+LICENSE=	GPLv2
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	ekg
+GH_TAGNAME=	bbc645f2f7966cb7b44446200c02627c3168b399
+
+MAKEFILE=	${FILESDIR}/Makefile
+INSTALL_TARGET=	install-strip
+
+.include <bsd.port.mk>

biology/fastahack/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1523600462
+SHA256 (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = dc8ef61765b7720fd2d163143696f1c82251bfd906ac5261642e7230d81d5da6
+SIZE (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = 18200

biology/fastahack/files/Makefile

@@ -0,0 +1,62 @@
+
+# Use ?= to allow overriding from the env or command-line, e.g.
+#
+#	make CXXFLAGS="-O3 -fPIC" install
+#
+# Package managers will override many of these variables automatically, so
+# this is aimed at making it easy to create packages (Debian packages,
+# FreeBSD ports, MacPorts, pkgsrc, etc.)
+
+CXX ?=		c++
+CXXFLAGS ?=	-O3
+DESTDIR ?=	stage
+PREFIX ?=	/usr/local
+STRIP ?=	strip
+INSTALL ?=	install -c
+MKDIR ?=	mkdir -p
+AR ?=		ar
+
+# Required flags that we shouldn't override
+# Must be compiler-independent
+CXXFLAGS +=	-D_FILE_OFFSET_BITS=64
+
+BIN =	fastahack
+LIB =	libfastahack.a
+OBJS =	Fasta.o split.o disorder.o
+MAIN =	FastaHack.o
+
+all:	$(BIN) $(LIB)
+
+$(BIN): $(OBJS) $(MAIN)
+	$(CXX) $(CXXFLAGS) $(OBJS) $(MAIN) -o $(BIN)
+
+$(LIB): $(OBJS)
+	${AR} -rs $(LIB) $(OBJS)
+
+FastaHack.o: Fasta.h FastaHack.cpp
+	$(CXX) $(CXXFLAGS) -c FastaHack.cpp
+
+Fasta.o: Fasta.h Fasta.cpp
+	$(CXX) $(CXXFLAGS) -c Fasta.cpp
+
+split.o: split.h split.cpp
+	$(CXX) $(CXXFLAGS) -c split.cpp
+
+disorder.o: disorder.c disorder.h
+	$(CXX) $(CXXFLAGS) -c disorder.c
+
+install: all
+	$(MKDIR) $(DESTDIR)$(PREFIX)/bin
+	$(MKDIR) $(DESTDIR)$(PREFIX)/include/fastahack
+	$(MKDIR) $(DESTDIR)$(PREFIX)/lib
+	$(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin
+	$(INSTALL) *.h $(DESTDIR)$(PREFIX)/include/fastahack
+	$(INSTALL) $(LIB) $(DESTDIR)$(PREFIX)/lib
+
+install-strip: install
+	$(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN)
+
+clean:
+	rm -rf $(BIN) $(LIB) $(OBJS) $(DESTDIR)
+
+.PHONY: clean

biology/fastahack/pkg-descr

@@ -0,0 +1,7 @@
+Fastahack is a small application for indexing and extracting sequences and
+subsequences from FASTA files.  The included Fasta.cpp library provides a FASTA
+reader and indexer that can be embedded into applications which would benefit
+from directly reading subsequences from FASTA files.  The library automatically
+handles index file generation and use.
+
+WWW: https://github.com/ekg/fastahack

biology/fastahack/pkg-plist

@@ -0,0 +1,7 @@
+bin/fastahack
+include/fastahack/Fasta.h
+include/fastahack/LargeFileSupport.h
+include/fastahack/Region.h
+include/fastahack/disorder.h
+include/fastahack/split.h
+lib/libfastahack.a