mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-27 00:57:50 +00:00
Update to 34.t25.d4.
PR: ports/93052 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
This commit is contained in:
Sam Lawrance
parent
c6004c8778
commit
f4cdc25a87
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=155633
@ -1,3 +1,4 @@
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# ex:ts=8
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# New ports collection makefile for: fasta3
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# Date created: 29 January 2001
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# Whom: Johann Visagie <johann@egenetics.com>
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@ -6,21 +7,25 @@
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#
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PORTNAME= fasta3
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PORTVERSION= 33.t08.d4
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PORTVERSION= 34.t25.d4
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/
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DISTNAME= fasta${PORTVERSION:S/.//g}
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EXTRACT_SUFX= .shar.Z
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MAINTAINER= fernan@iib.unsam.edu.ar
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COMMENT= A collection of programs for searching DNA and protein databases, v3
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COMMENT= A collection of programs for searching DNA and protein databases
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NO_CDROM= May not be sold or incorporated into a commercial product
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WRKSRC= ${WRKDIR}/fasta3
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PKGMESSAGE= ${WRKDIR}/pkg-message
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FASTA3_DOCDIR= ${PREFIX}/share/doc/fasta3
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FASTA3_DOCS= 00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \
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readme.*
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NO_CDROM= "May not be sold or incorporated into a commercial product"
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WRKSRC= ${WRKDIR}/${PORTNAME}
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SUB_FILES= pkg-message
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MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS}
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FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
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fasta20.doc fasta_func.doc readme.* fasta.defaults
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DATA= *.mat
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EXAMPLES= *.aa *.lc *.seq
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MAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
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MLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \
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@ -35,19 +40,24 @@ do-extract:
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done
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post-install:
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@ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
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${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
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@ ${MKDIR} ${DATADIR}
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.for data in ${DATA}
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${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
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.endfor
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@ ${MKDIR} ${EXAMPLESDIR}
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.for ex in ${EXAMPLES}
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${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
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.endfor
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.for manpage in ${MAN1}
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@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
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.endfor
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.if !defined(NOPORTDOCS)
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@ ${MKDIR} ${FASTA3_DOCDIR}
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@ ${MKDIR} ${DOCSDIR}
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.for docfile in ${FASTA3_DOCS}
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@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR}
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@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
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.endfor
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.endif
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.if !defined(BATCH)
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@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
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@ ${CAT} ${PKGMESSAGE}
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.endif
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.include <bsd.port.mk>
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@ -1,3 +1,3 @@
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MD5 (fasta33t08d4.shar.Z) = e6217268e122b2ca7c51b443425e40e3
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SHA256 (fasta33t08d4.shar.Z) = f2eb329393cd330c6848cff2a147fcc2c2f74dff6033cf7ba70177ab4bcca231
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SIZE (fasta33t08d4.shar.Z) = 685912
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MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7
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SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe
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SIZE (fasta34t25d4.shar.Z) = 799416
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@ -1,49 +1,33 @@
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--- Makefile.orig Mon May 7 11:36:23 2001
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+++ Makefile Mon May 7 11:40:36 2001
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@@ -12,13 +12,13 @@
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# use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
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-CC= cc -O -std1
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+#CC= cc -O -std1
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#CC= insure -g -DDEBUG
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#CC= cc -g -DDEBUG -std1
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#CC= gcc -g -Wall
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--- Makefile.orig Thu Feb 9 12:03:37 2006
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+++ Makefile Thu Feb 9 12:07:21 2006
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@@ -7,7 +7,7 @@
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# in dropnfa.c (wrp 3/19/1998)
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#
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# standard line for normal searching
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-CFLAGS= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
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+CFLAGS+= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
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-CC= gcc -g -O3
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+#CC= gcc -g -O3
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#CC=gcc -Wall -pedantic -ansi -g -O
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#CC = gcc -g -DDEBUG
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#CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG
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@@ -21,7 +21,7 @@
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#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
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# standard options
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-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
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+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
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# -I/usr/local/include/mysql -DMYSQL_DB
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#(for mySQL databases) (also requires change to Makefile33.common)
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#
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#(for mySQL databases) (also requires change to Makefile34.common)
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@@ -35,10 +35,10 @@
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@@ -32,11 +32,15 @@
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HFLAGS= -o
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NFLAGS= -o
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-#for DEC Unix V4.0
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THR_SUBS = pthr_subs
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-THR_LIBS = -threads
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+THR_LIBS = -pthread
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# for Linux
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THR_SUBS = pthr_subs2
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-THR_LIBS = -lpthread
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+#THR_LIBS = -lpthread
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THR_CC =
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+#for DEC Unix V4.0
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+#THR_SUBS = pthr_subs
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+#THR_LIBS = -threads
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+#THR_CC =
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+#
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#for Sun
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#THR_SUBS = uthr_subs
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#THR_LIBS = -lthread
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@@ -53,9 +57,9 @@
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#THR_LIBS = -lpthreads
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#THR_CC =
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-XDIR = /seqprg/slib/bin
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-XDIR = /seqprg/bin
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+XDIR = ${PREFIX}/bin
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# renamed (fasta33) programs
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-include Makefile33.common
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+#include Makefile33.common
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# conventional (fasta3) names
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-#include Makefile.common
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+include Makefile.common
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DROPNFA_O = drop_nfa.o
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DROPGSW_O = dropgsw.o
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@ -1,20 +0,0 @@
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--- Makefile.common.orig Mon Jan 29 12:42:32 2001
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+++ Makefile.common Mon Jan 29 13:44:06 2001
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@@ -46,7 +46,7 @@
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XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t
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XPROGS = fastx33 tfastx33 fasty33 tfasty33
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-PROGS = $(SPROGS) $(TPROGS)
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+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS)
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all : $(PROGS)
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@@ -60,7 +60,7 @@
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rm -f *.o $(PROGS)
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install:
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- cp $(PROGS) $(XDIR)
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+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR)
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sinstall:
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cp $(SPROGS) $(XDIR)
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@ -1,11 +0,0 @@
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--- comp_thr.c.orig Thu Aug 22 20:32:10 2002
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+++ comp_thr.c Thu Aug 22 20:32:25 2002
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@@ -16,7 +16,7 @@
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#include <time.h>
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#ifdef UNIX
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-#if !defined(__NetBSD__) && !defined(MacOSX)
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+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
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#include <values.h>
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#else
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#include <limits.h>
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@ -1,11 +0,0 @@
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--- compacc.c.orig Thu Aug 22 20:30:30 2002
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+++ compacc.c Thu Aug 22 20:30:43 2002
|
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@@ -11,7 +11,7 @@
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#if defined(UNIX) || defined(MSDOS)
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#include <sys/types.h>
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#endif
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-#if !defined(__MWERKS__) && !defined(MacOSX)
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+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
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#include <values.h>
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#else
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#include <limits.h>
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@ -1,11 +0,0 @@
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||||
--- complib.c.orig Thu Aug 22 20:33:57 2002
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+++ complib.c Thu Aug 22 20:34:07 2002
|
||||
@@ -29,7 +29,7 @@
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#include <ctype.h>
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#include <time.h>
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#ifdef UNIX
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-#if !defined(__NetBSD__) && !defined(MacOSX)
|
||||
+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
|
||||
#include <values.h>
|
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#else
|
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#include <limits.h>
|
||||
@ -1,11 +0,0 @@
|
||||
--- scaleswn.c.orig Thu Aug 22 20:30:55 2002
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+++ scaleswn.c Thu Aug 22 20:31:06 2002
|
||||
@@ -26,7 +26,7 @@
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||||
#include <math.h>
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#include <string.h>
|
||||
|
||||
-#if !defined(__MWERKS__) && !defined(MacOSX)
|
||||
+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
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||||
#include <values.h>
|
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#else
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#include <limits.h> /* needed for LONG_MAX */
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||||
16
biology/fasta3/files/pkg-message.in
Normal file
16
biology/fasta3/files/pkg-message.in
Normal file
@ -0,0 +1,16 @@
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=============================================================================
|
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|
||||
The FASTA3 package has been successfully installed.
|
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||||
A sample configuration file has been installed to
|
||||
%%PREFIX%%/etc
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as "fastlibs.sample". This may be renamed to "fastlibs" and edited
|
||||
to suit the requirements of a particular site.
|
||||
|
||||
In order to use the FASTA3 programs, a user must set the environment
|
||||
variable FASTLIBS to contain the full path of the FASTA3 configuration
|
||||
file, e.g.:
|
||||
|
||||
set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
|
||||
|
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==============================================================================
|
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@ -1,15 +0,0 @@
|
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--------------------------------------------------------------------------
|
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|
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The FASTA3 package has been successfully installed.
|
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|
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NB: A sample configuration file has been installed to %%PREFIX%%/etc as
|
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"fastlibs.sample". This may be renamed to "fastlibs" and edited
|
||||
to suit the requirements of a particular site.
|
||||
|
||||
In order to use the FASTA3 programs, a user must set the environment
|
||||
variable FASTLIBS to contain the full path of the FASTA3 configuration
|
||||
file, e.g.:
|
||||
|
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- set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
|
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|
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--------------------------------------------------------------------------
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@ -1,11 +1,41 @@
|
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%%PORTDOCS%%%%DOCSDIR%%/00README.1st
|
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%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
|
||||
bin/fasta34
|
||||
bin/prss34_t
|
||||
bin/tfastf34_t
|
||||
bin/fastf34_t
|
||||
bin/fastm34_t
|
||||
bin/tfasts34_t
|
||||
bin/tfasty34_t
|
||||
bin/fasty34_t
|
||||
bin/tfastx34_t
|
||||
bin/fastx34_t
|
||||
bin/tfasta34_t
|
||||
bin/fasts34_t
|
||||
bin/fasta34_t
|
||||
bin/ssearch34_t
|
||||
bin/tfastf34
|
||||
bin/fastf34
|
||||
bin/prfx34
|
||||
bin/prss34
|
||||
bin/tfastm34
|
||||
bin/fastm34
|
||||
bin/tfasts34
|
||||
bin/tfasty34
|
||||
bin/fasty34
|
||||
bin/tfastx34
|
||||
bin/fastx34
|
||||
bin/fasts34
|
||||
bin/tfasta34
|
||||
bin/ssearch34
|
||||
bin/prfx34_t
|
||||
etc/fastlibs.sample
|
||||
%%PORTDOCS%%%%DOCSDIR%%/README
|
||||
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
|
||||
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
|
||||
%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
|
||||
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.me
|
||||
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
|
||||
%%PORTDOCS%%%%DOCSDIR%%/fasta20.doc
|
||||
%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_2.0
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.0
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4
|
||||
@ -16,30 +46,57 @@
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.v31t1
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.v32t0
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
|
||||
%%PORTDOCS%%%%DOCSDIR%%/readme.w32
|
||||
bin/fasta3
|
||||
bin/fasta3_t
|
||||
bin/fastf3
|
||||
bin/fastf3_t
|
||||
bin/fasts3
|
||||
bin/fasts3_t
|
||||
bin/fastx3
|
||||
bin/fastx3_t
|
||||
bin/fasty3
|
||||
bin/fasty3_t
|
||||
bin/map_db
|
||||
bin/prss3
|
||||
bin/ssearch3
|
||||
bin/ssearch3_t
|
||||
bin/tfasta3
|
||||
bin/tfasta3_t
|
||||
bin/tfastf3
|
||||
bin/tfastf3_t
|
||||
bin/tfasts3
|
||||
bin/tfasts3_t
|
||||
bin/tfastx3
|
||||
bin/tfastx3_t
|
||||
bin/tfasty3
|
||||
bin/tfasty3_t
|
||||
etc/fastlibs.sample
|
||||
%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
|
||||
%%EXAMPLESDIR%%/egmsmg.aa
|
||||
%%EXAMPLESDIR%%/gtm1_human.aa
|
||||
%%EXAMPLESDIR%%/gtt1_drome.aa
|
||||
%%EXAMPLESDIR%%/h10_human.aa
|
||||
%%EXAMPLESDIR%%/hahu.aa
|
||||
%%EXAMPLESDIR%%/lcbo.aa
|
||||
%%EXAMPLESDIR%%/m1r.aa
|
||||
%%EXAMPLESDIR%%/m2.aa
|
||||
%%EXAMPLESDIR%%/mchu.aa
|
||||
%%EXAMPLESDIR%%/mgstm1.aa
|
||||
%%EXAMPLESDIR%%/ms1.aa
|
||||
%%EXAMPLESDIR%%/musplfm.aa
|
||||
%%EXAMPLESDIR%%/mwkw.aa
|
||||
%%EXAMPLESDIR%%/mwrtc1.aa
|
||||
%%EXAMPLESDIR%%/n0.aa
|
||||
%%EXAMPLESDIR%%/n1.aa
|
||||
%%EXAMPLESDIR%%/n2.aa
|
||||
%%EXAMPLESDIR%%/n2s.aa
|
||||
%%EXAMPLESDIR%%/n2t.aa
|
||||
%%EXAMPLESDIR%%/ngt.aa
|
||||
%%EXAMPLESDIR%%/ngts.aa
|
||||
%%EXAMPLESDIR%%/oohu.aa
|
||||
%%EXAMPLESDIR%%/prio_atepa.aa
|
||||
%%EXAMPLESDIR%%/qrhuld.aa
|
||||
%%EXAMPLESDIR%%/xurt8c.aa
|
||||
%%EXAMPLESDIR%%/xurtg.aa
|
||||
%%EXAMPLESDIR%%/mgstm1.lc
|
||||
%%EXAMPLESDIR%%/xurt8c.lc
|
||||
%%EXAMPLESDIR%%/bovgh.seq
|
||||
%%EXAMPLESDIR%%/bovprl.seq
|
||||
%%EXAMPLESDIR%%/gst.seq
|
||||
%%EXAMPLESDIR%%/hsgstm1b.seq
|
||||
%%EXAMPLESDIR%%/humgstd.seq
|
||||
%%EXAMPLESDIR%%/mgstm1.seq
|
||||
%%EXAMPLESDIR%%/mgtt2_x.seq
|
||||
%%DATADIR%%/blosum45.mat
|
||||
%%DATADIR%%/blosum50.mat
|
||||
%%DATADIR%%/blosum62.mat
|
||||
%%DATADIR%%/blosum80.mat
|
||||
%%DATADIR%%/dna.mat
|
||||
%%DATADIR%%/idn_aa.mat
|
||||
%%DATADIR%%/md_10.mat
|
||||
%%DATADIR%%/md_20.mat
|
||||
%%DATADIR%%/md_40.mat
|
||||
%%DATADIR%%/pam120.mat
|
||||
%%DATADIR%%/pam250.mat
|
||||
%%DATADIR%%/rna.mat
|
||||
%%DATADIR%%/vtml160.mat
|
||||
%%PORTDOCS%%@dirrm %%DOCSDIR%%
|
||||
@dirrm %%EXAMPLESDIR%%
|
||||
@dirrm %%DATADIR%%
|
||||
|
||||
Loading…
Reference in New Issue
Block a user