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| author | Ruslan Makhmatkhanov <rm@FreeBSD.org> | 2015-09-25 18:37:24 +0000 |
|---|---|---|
| committer | Ruslan Makhmatkhanov <rm@FreeBSD.org> | 2015-09-25 18:37:24 +0000 |
| commit | e20b08bbfc9e31ec7e94169dffc0abe1ed290e66 (patch) | |
| tree | 453b7c4208bd738ff634cd0b923b2f7130515d6f /biology/cdbfasta | |
| parent | 835d05fd2c1896ac0deb3224422e505b26fc3af9 (diff) | |
| download | ports-e20b08bbfc9e31ec7e94169dffc0abe1ed290e66.tar.gz ports-e20b08bbfc9e31ec7e94169dffc0abe1ed290e66.zip | |
Fast indexing and retrieval of FASTA records from flat file data bases.
WWW: http://sourceforge.net/projects/cdbfasta/
PR: 203233
Submitted by: Jason Bacon <jwbacon@tds.net>
Notes
Notes:
svn path=/head/; revision=397850
Diffstat (limited to 'biology/cdbfasta')
| -rw-r--r-- | biology/cdbfasta/Makefile | 25 | ||||
| -rw-r--r-- | biology/cdbfasta/distinfo | 2 | ||||
| -rw-r--r-- | biology/cdbfasta/files/patch-Makefile | 54 | ||||
| -rw-r--r-- | biology/cdbfasta/pkg-descr | 3 |
4 files changed, 84 insertions, 0 deletions
diff --git a/biology/cdbfasta/Makefile b/biology/cdbfasta/Makefile new file mode 100644 index 000000000000..149b07e13181 --- /dev/null +++ b/biology/cdbfasta/Makefile @@ -0,0 +1,25 @@ +# Created by: Dan Siercks <dsiercks@uwm.edu> +# $FreeBSD$ + +PORTNAME= cdbfasta +PORTVERSION= 2010.07.22 +CATEGORIES= biology +MASTER_SITES= http://acadix.biz/Ports/distfiles/ \ + http://personalpages.tds.net/~jwbacon/Ports/distfiles/ + +MAINTAINER= jwbacon@tds.net +COMMENT= Fast indexing and retrieval of FASTA records from flat file databases + +# LICENSE= unspecified + +WRKSRC= ${WRKDIR}/${PORTNAME} + +USES= gmake + +PLIST_FILES= bin/cdbfasta bin/cdbyank + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/cdbfasta ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/cdbyank ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/cdbfasta/distinfo b/biology/cdbfasta/distinfo new file mode 100644 index 000000000000..0d3ec1700289 --- /dev/null +++ b/biology/cdbfasta/distinfo @@ -0,0 +1,2 @@ +SHA256 (cdbfasta-2010.07.22.tar.gz) = 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c +SIZE (cdbfasta-2010.07.22.tar.gz) = 59735 diff --git a/biology/cdbfasta/files/patch-Makefile b/biology/cdbfasta/files/patch-Makefile new file mode 100644 index 000000000000..c062b13bf9eb --- /dev/null +++ b/biology/cdbfasta/files/patch-Makefile @@ -0,0 +1,54 @@ +--- Makefile.orig 2009-12-03 20:17:51 UTC ++++ Makefile +@@ -18,7 +18,10 @@ else + MARCH = + endif + +-CC := g++ ++# Use the correct compiler (CXX, not CC) and respect the environment ++# by using ?= ++CXX ?= g++ ++ + BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \ + -D_REENTRANT +@@ -33,30 +36,30 @@ else + endif + + ifeq ($(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 + +-LINKER := g++ +-LDFLAGS = -lz ++LINKER := ${CXX} ++LDFLAGS = -lz + #if ENABLE_COMPRESSION is not needed, + # LDFLAGS = + diff --git a/biology/cdbfasta/pkg-descr b/biology/cdbfasta/pkg-descr new file mode 100644 index 000000000000..30e345465089 --- /dev/null +++ b/biology/cdbfasta/pkg-descr @@ -0,0 +1,3 @@ +Fast indexing and retrieval of FASTA records from flat file data bases. + +WWW: http://sourceforge.net/projects/cdbfasta/ |