svn commit: r397850 - in head/biology: . cdbfasta cdbfasta/files
Ruslan Makhmatkhanov
rm at FreeBSD.org
Fri Sep 25 18:37:26 UTC 2015
Author: rm
Date: Fri Sep 25 18:37:24 2015
New Revision: 397850
URL: https://svnweb.freebsd.org/changeset/ports/397850
Log:
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 at tds.net>
Added:
head/biology/cdbfasta/
head/biology/cdbfasta/Makefile (contents, props changed)
head/biology/cdbfasta/distinfo (contents, props changed)
head/biology/cdbfasta/files/
head/biology/cdbfasta/files/patch-Makefile (contents, props changed)
head/biology/cdbfasta/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Fri Sep 25 18:35:14 2015 (r397849)
+++ head/biology/Makefile Fri Sep 25 18:37:24 2015 (r397850)
@@ -12,6 +12,7 @@
SUBDIR += biojava
SUBDIR += blat
SUBDIR += cd-hit
+ SUBDIR += cdbfasta
SUBDIR += chemeq
SUBDIR += clustalw
SUBDIR += consed
Added: head/biology/cdbfasta/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/cdbfasta/Makefile Fri Sep 25 18:37:24 2015 (r397850)
@@ -0,0 +1,25 @@
+# Created by: Dan Siercks <dsiercks at 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 at 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>
Added: head/biology/cdbfasta/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/cdbfasta/distinfo Fri Sep 25 18:37:24 2015 (r397850)
@@ -0,0 +1,2 @@
+SHA256 (cdbfasta-2010.07.22.tar.gz) = 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c
+SIZE (cdbfasta-2010.07.22.tar.gz) = 59735
Added: head/biology/cdbfasta/files/patch-Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/cdbfasta/files/patch-Makefile Fri Sep 25 18:37:24 2015 (r397850)
@@ -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 =
+
Added: head/biology/cdbfasta/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/cdbfasta/pkg-descr Fri Sep 25 18:37:24 2015 (r397850)
@@ -0,0 +1,3 @@
+Fast indexing and retrieval of FASTA records from flat file data bases.
+
+WWW: http://sourceforge.net/projects/cdbfasta/
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