From edab74313c449f0cd86473a96695cf4ee180b285 Mon Sep 17 00:00:00 2001 From: Sergey Matveychuk Date: Sun, 7 May 2006 16:52:33 +0000 Subject: - Update to 34.t25.d6 PR: ports/96063 Submitted by: maintainer --- biology/fasta3/Makefile | 12 +++++-- biology/fasta3/distinfo | 6 ++-- biology/fasta3/files/Makefile.freebsd | 67 +++++++++++++++++++++++++++++++++++ biology/fasta3/files/patch-Makefile | 33 ----------------- 4 files changed, 80 insertions(+), 38 deletions(-) create mode 100644 biology/fasta3/files/Makefile.freebsd delete mode 100644 biology/fasta3/files/patch-Makefile (limited to 'biology/fasta3') diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile index 9b1eeef3ae98..f15f6141aaac 100644 --- a/biology/fasta3/Makefile +++ b/biology/fasta3/Makefile @@ -7,7 +7,7 @@ # PORTNAME= fasta3 -PORTVERSION= 34.t25.d5 +PORTVERSION= 34.t25.d6 CATEGORIES= biology MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/ DISTNAME= fasta${PORTVERSION:S/.//g} @@ -19,8 +19,13 @@ COMMENT= A collection of programs for searching DNA and protein databases NO_CDROM= "May not be sold or incorporated into a commercial product" WRKSRC= ${WRKDIR}/${PORTNAME} SUB_FILES= pkg-message +MAKEFILE= Makefile.freebsd -MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} +XDIR= ${PREFIX}/bin +FASTA_HOST!= /usr/bin/uname -n + +MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \ + FASTA_HOST='"${FASTA_HOST}"' FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \ fasta20.doc fasta_func.doc readme.* fasta.defaults @@ -39,6 +44,9 @@ do-extract: cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \ done +post-extract: + @ cp ${FILESDIR}/Makefile.freebsd ${WRKSRC} + post-install: ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample @ ${MKDIR} ${DATADIR} diff --git a/biology/fasta3/distinfo b/biology/fasta3/distinfo index c277112983b1..59552fe2f1bd 100644 --- a/biology/fasta3/distinfo +++ b/biology/fasta3/distinfo @@ -1,3 +1,3 @@ -MD5 (fasta34t25d5.shar.Z) = 500a449fe3eeebbeb3e7f53f652505c7 -SHA256 (fasta34t25d5.shar.Z) = bcb7c25b6e3d883cc4c61c35b94b4dc42c49a158859cfefbf6a3f9357c0e7482 -SIZE (fasta34t25d5.shar.Z) = 795675 +MD5 (fasta34t25d6.shar.Z) = 462419371d55afd787043d2104c461cc +SHA256 (fasta34t25d6.shar.Z) = 409abdf657931cb07ea2ae38587d9387d418436662f1c1b889a3829302656449 +SIZE (fasta34t25d6.shar.Z) = 798483 diff --git a/biology/fasta3/files/Makefile.freebsd b/biology/fasta3/files/Makefile.freebsd new file mode 100644 index 000000000000..5bd489001187 --- /dev/null +++ b/biology/fasta3/files/Makefile.freebsd @@ -0,0 +1,67 @@ +# +# Makefile for building fasta3 on FreeBSD +# +# Fernan Aguero - + +# we take care of doing variable assignment using the '?=' and '+=' +# operators to preserve the value of variables if they are already +# defined. In FreeBSD this happens when fasta3 is build from the port or +# when the user has set these variables -- most notably CC and/or CFLAGS +# -- in /etc/make.conf + +# Compiler executable, and optional flags +CC?= gcc +CFLAGS?= -g -O2 + +# your FASTA host +FASTA_HOST?= "your_fasta_host" + +# common CFLAGS. These are the set of CFLAGS that are always used +COMMON_CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \ + -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \ + -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \ + -DHAS_INTTYPES -DSAMP_STATS + +# standard options, these will be added to the common CFLAGS if +# selected below +STANDARD_CFLAGS= -DSFCHAR="':'" -DFASTA_HOST='${FASTA_HOST}' \ + -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC + +# options for superfamily validations, these will be added to the common +# CFLAGS if selected below +SUPERFAMILY_CFLAGS= -DSFCHAR="'|'" -DSUPERFAMNUM -DBIG_LIB64 + +# here we define CFLAGS to be the sum of common flags plus a subset of +# optional flags that define our intended use. +# The default standard flags are selected by default, although the user +# can override this if s/he wants +CFLAGS+= ${COMMON_CFLAGS} ${STANDARD_CFLAGS} + +XDIR?= /usr/local/bin + +LIB_M+= -lm + +HFLAGS+= -o +NFLAGS+= -o + + + +# FreeBSD users BEWARE! Different threading models ahead! + +# The threading model has changed along the way from FreeBSD-4 to +# FreeBSD-6. If you're building fasta3 on your own, you will need to +# adjust this accordingly. The default works in FreeBSD-6x (currently +# the recommended major version for use in production). Or better yet, +# use the biology/fasta3 port from the ports collection, which will use +# the correct threading library for your OSVERSION + +THR_SUBS?= pthr_subs2 +THR_LIBS?= -lpthread +THR_CC?= + +DROPNFA_O = drop_nfa.o +DROPGSW_O = dropgsw.o +DROPRSS_O = dropnsw.o +DROPTFA_O = drop_tfa.o + +include Makefile34m.common diff --git a/biology/fasta3/files/patch-Makefile b/biology/fasta3/files/patch-Makefile deleted file mode 100644 index 60b18c9b84a0..000000000000 --- a/biology/fasta3/files/patch-Makefile +++ /dev/null @@ -1,33 +0,0 @@ ---- Makefile.orig Thu Feb 9 12:03:37 2006 -+++ Makefile Thu Feb 9 12:07:21 2006 -@@ -7,7 +7,7 @@ - # in dropnfa.c (wrp 3/19/1998) - # - --CC= gcc -g -O3 -+#CC= gcc -g -O3 - #CC=gcc -Wall -pedantic -ansi -g -O - #CC = gcc -g -DDEBUG - #CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG -@@ -21,7 +21,7 @@ - #CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'|'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DSUPERFAMNUM -DUSE_MMAP -D_REENTRANT -DBIG_LIB64 -D_LARGE_FILE_SOURCE -DUSE_FSEEKO -D_FILE_OFFSET_BITS=64 -DHAS_INTTYPES -DSAMP_STATS - - # standard options --CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -+CFLAGS+= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC - # -I/usr/local/include/mysql -DMYSQL_DB - # - #(for mySQL databases) (also requires change to Makefile34.common) -@@ -35,10 +35,10 @@ - - # for Linux - THR_SUBS = pthr_subs2 --THR_LIBS = -lpthread -+#THR_LIBS = -lpthread - THR_CC = - --XDIR = /seqprg/bin -+XDIR = ${PREFIX}/bin - - DROPNFA_O = drop_nfa.o - DROPGSW_O = dropgsw.o -- cgit v1.2.3