diff -ruN /usr/ports/biology/fasta3/Makefile fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile Thu Jul 1 00:02:23 2004 +++ fasta3/Makefile Thu Feb 9 12:03:30 2006 @@ -1,3 +1,4 @@ +# ex:ts=8 # New ports collection makefile for: fasta3 # Date created: 29 January 2001 # Whom: Johann Visagie @@ -6,21 +7,25 @@ # PORTNAME= fasta3 -PORTVERSION= 33.t08.d4 +PORTVERSION= 34.t25.d4 CATEGORIES= biology MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/ DISTNAME= fasta${PORTVERSION:S/.//g} EXTRACT_SUFX= .shar.Z MAINTAINER= fernan@iib.unsam.edu.ar -COMMENT= A collection of programs for searching DNA and protein databases, v3 +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}/fasta3 -PKGMESSAGE= ${WRKDIR}/pkg-message -FASTA3_DOCDIR= ${PREFIX}/share/doc/fasta3 -FASTA3_DOCS= 00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \ - readme.* +NO_CDROM= "May not be sold or incorporated into a commercial product" +WRKSRC= ${WRKDIR}/${PORTNAME} +SUB_FILES= pkg-message + +MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} + +FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \ + fasta20.doc fasta_func.doc readme.* fasta.defaults +DATA= *.mat +EXAMPLES= *.aa *.lc *.seq MAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1 MLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \ @@ -35,19 +40,24 @@ done post-install: - @ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample + ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample + @ ${MKDIR} ${DATADIR} +.for data in ${DATA} + ${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR} +.endfor + @ ${MKDIR} ${EXAMPLESDIR} +.for ex in ${EXAMPLES} + ${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR} +.endfor .for manpage in ${MAN1} @ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/ .endfor .if !defined(NOPORTDOCS) - @ ${MKDIR} ${FASTA3_DOCDIR} + @ ${MKDIR} ${DOCSDIR} .for docfile in ${FASTA3_DOCS} - @ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR} + @ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR} .endfor .endif -.if !defined(BATCH) - @ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE} @ ${CAT} ${PKGMESSAGE} -.endif .include diff -ruN /usr/ports/biology/fasta3/distinfo fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo Wed Jan 25 11:31:47 2006 +++ fasta3/distinfo Sat Feb 4 18:24:02 2006 @@ -1,3 +1,3 @@ -MD5 (fasta33t08d4.shar.Z) = e6217268e122b2ca7c51b443425e40e3 -SHA256 (fasta33t08d4.shar.Z) = f2eb329393cd330c6848cff2a147fcc2c2f74dff6033cf7ba70177ab4bcca231 -SIZE (fasta33t08d4.shar.Z) = 685912 +MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7 +SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe +SIZE (fasta34t25d4.shar.Z) = 799416 diff -ruN /usr/ports/biology/fasta3/files/patch-Makefile fasta3/files/patch-Makefile --- /usr/ports/biology/fasta3/files/patch-Makefile Mon May 7 09:16:33 2001 +++ fasta3/files/patch-Makefile Thu Feb 9 12:07:23 2006 @@ -1,49 +1,33 @@ ---- Makefile.orig Mon May 7 11:36:23 2001 -+++ Makefile Mon May 7 11:40:36 2001 -@@ -12,13 +12,13 @@ - - # use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files - --CC= cc -O -std1 -+#CC= cc -O -std1 - #CC= insure -g -DDEBUG - #CC= cc -g -DDEBUG -std1 - #CC= gcc -g -Wall +--- 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) # - # standard line for normal searching --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 -+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 - # -I/usr/local/include/mysql -DMYSQL_DB - #(for mySQL databases) (also requires change to Makefile33.common) -@@ -32,11 +32,15 @@ - HFLAGS= -o - NFLAGS= -o +-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 DEC Unix V4.0 - THR_SUBS = pthr_subs --THR_LIBS = -threads -+THR_LIBS = -pthread + # for Linux + THR_SUBS = pthr_subs2 +-THR_LIBS = -lpthread ++#THR_LIBS = -lpthread THR_CC = -+#for DEC Unix V4.0 -+#THR_SUBS = pthr_subs -+#THR_LIBS = -threads -+#THR_CC = -+# - #for Sun - #THR_SUBS = uthr_subs - #THR_LIBS = -lthread -@@ -53,9 +57,9 @@ - #THR_LIBS = -lpthreads - #THR_CC = - --XDIR = /seqprg/slib/bin +-XDIR = /seqprg/bin +XDIR = ${PREFIX}/bin - # renamed (fasta33) programs --include Makefile33.common -+#include Makefile33.common - # conventional (fasta3) names --#include Makefile.common -+include Makefile.common + DROPNFA_O = drop_nfa.o + DROPGSW_O = dropgsw.o diff -ruN /usr/ports/biology/fasta3/files/patch-Makefile.common fasta3/files/patch-Makefile.common --- /usr/ports/biology/fasta3/files/patch-Makefile.common Sun Feb 11 13:28:59 2001 +++ fasta3/files/patch-Makefile.common Wed Dec 31 21:00:00 1969 @@ -1,20 +0,0 @@ ---- Makefile.common.orig Mon Jan 29 12:42:32 2001 -+++ Makefile.common Mon Jan 29 13:44:06 2001 -@@ -46,7 +46,7 @@ - XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t - XPROGS = fastx33 tfastx33 fasty33 tfasty33 - --PROGS = $(SPROGS) $(TPROGS) -+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS) - - all : $(PROGS) - -@@ -60,7 +60,7 @@ - rm -f *.o $(PROGS) - - install: -- cp $(PROGS) $(XDIR) -+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR) - - sinstall: - cp $(SPROGS) $(XDIR) diff -ruN /usr/ports/biology/fasta3/files/patch-comp_thr.c fasta3/files/patch-comp_thr.c --- /usr/ports/biology/fasta3/files/patch-comp_thr.c Fri Aug 23 00:36:33 2002 +++ fasta3/files/patch-comp_thr.c Wed Dec 31 21:00:00 1969 @@ -1,11 +0,0 @@ ---- comp_thr.c.orig Thu Aug 22 20:32:10 2002 -+++ comp_thr.c Thu Aug 22 20:32:25 2002 -@@ -16,7 +16,7 @@ - #include - - #ifdef UNIX --#if !defined(__NetBSD__) && !defined(MacOSX) -+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX) - #include - #else - #include diff -ruN /usr/ports/biology/fasta3/files/patch-compacc.c fasta3/files/patch-compacc.c --- /usr/ports/biology/fasta3/files/patch-compacc.c Fri Aug 23 00:36:33 2002 +++ fasta3/files/patch-compacc.c Wed Dec 31 21:00:00 1969 @@ -1,11 +0,0 @@ ---- compacc.c.orig Thu Aug 22 20:30:30 2002 -+++ compacc.c Thu Aug 22 20:30:43 2002 -@@ -11,7 +11,7 @@ - #if defined(UNIX) || defined(MSDOS) - #include - #endif --#if !defined(__MWERKS__) && !defined(MacOSX) -+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX) - #include - #else - #include diff -ruN /usr/ports/biology/fasta3/files/patch-complib.c fasta3/files/patch-complib.c --- /usr/ports/biology/fasta3/files/patch-complib.c Fri Aug 23 00:36:33 2002 +++ fasta3/files/patch-complib.c Wed Dec 31 21:00:00 1969 @@ -1,11 +0,0 @@ ---- complib.c.orig Thu Aug 22 20:33:57 2002 -+++ complib.c Thu Aug 22 20:34:07 2002 -@@ -29,7 +29,7 @@ - #include - #include - #ifdef UNIX --#if !defined(__NetBSD__) && !defined(MacOSX) -+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX) - #include - #else - #include diff -ruN /usr/ports/biology/fasta3/files/patch-scaleswn.c fasta3/files/patch-scaleswn.c --- /usr/ports/biology/fasta3/files/patch-scaleswn.c Fri Aug 23 00:36:33 2002 +++ fasta3/files/patch-scaleswn.c Wed Dec 31 21:00:00 1969 @@ -1,11 +0,0 @@ ---- scaleswn.c.orig Thu Aug 22 20:30:55 2002 -+++ scaleswn.c Thu Aug 22 20:31:06 2002 -@@ -26,7 +26,7 @@ - #include - #include - --#if !defined(__MWERKS__) && !defined(MacOSX) -+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX) - #include - #else - #include /* needed for LONG_MAX */ diff -ruN /usr/ports/biology/fasta3/files/pkg-message.in fasta3/files/pkg-message.in --- /usr/ports/biology/fasta3/files/pkg-message.in Wed Dec 31 21:00:00 1969 +++ fasta3/files/pkg-message.in Sun Feb 5 00:27:29 2006 @@ -0,0 +1,16 @@ +============================================================================= + + The FASTA3 package has been successfully installed. + + A sample configuration file has been installed to + %%PREFIX%%/etc + 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" + +============================================================================== diff -ruN /usr/ports/biology/fasta3/pkg-message fasta3/pkg-message --- /usr/ports/biology/fasta3/pkg-message Sun Feb 11 13:28:59 2001 +++ fasta3/pkg-message Wed Dec 31 21:00:00 1969 @@ -1,15 +0,0 @@ --------------------------------------------------------------------------- - -The FASTA3 package has been successfully installed. - -NB: A sample configuration file has been installed to %%PREFIX%%/etc 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" - --------------------------------------------------------------------------- diff -ruN /usr/ports/biology/fasta3/pkg-plist fasta3/pkg-plist --- /usr/ports/biology/fasta3/pkg-plist Wed Oct 22 06:29:51 2003 +++ fasta3/pkg-plist Thu Feb 9 12:12:48 2006 @@ -1,11 +1,41 @@ -%%PORTDOCS%%%%DOCSDIR%%/00README.1st -%%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%%