diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/fasta3/Makefile | 52 | ||||
| -rw-r--r-- | biology/fasta3/distinfo | 1 | ||||
| -rw-r--r-- | biology/fasta3/files/patch-Makefile | 49 | ||||
| -rw-r--r-- | biology/fasta3/files/patch-Makefile.common | 20 | ||||
| -rw-r--r-- | biology/fasta3/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/fasta3/pkg-descr | 20 | ||||
| -rw-r--r-- | biology/fasta3/pkg-message | 15 | ||||
| -rw-r--r-- | biology/fasta3/pkg-plist | 45 |
9 files changed, 204 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 0e5e7c5dfae0..880d5e36e467 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -8,6 +8,7 @@ SUBDIR += deft SUBDIR += emboss SUBDIR += fasta + SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += gaussian98 SUBDIR += gperiodic diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile new file mode 100644 index 000000000000..c7b27e097cab --- /dev/null +++ b/biology/fasta3/Makefile @@ -0,0 +1,52 @@ +# New ports collection makefile for: fasta3 +# Date created: 29 January 2001 +# Whom: Johann Visagie <johann@egenetics.com> +# +# $FreeBSD$ +# + +PORTNAME= fasta3 +PORTVERSION= 33.t08 +CATEGORIES= biology +MASTER_SITES= http://ftp.virginia.edu/pub/fasta/ +DISTNAME= fasta${PORTVERSION:S/.//g} +EXTRACT_SUFX= .shar.Z + +MAINTAINER= johann@egenetics.com + +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.* + +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 \ + fasta3.1 fasty3.1 fasta3.1 tfasty3.1 fasta3.1 ssearch3.1 \ + fastf3.1 tfastf3.1 fasts3.1 tfasts3.1 + +do-extract: + @ ${RM} -rf ${WRKDIR} + @ ${MKDIR} ${WRKSRC} + @ for file in ${EXTRACT_ONLY}; do \ + cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \ + done + +post-install: + @ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample +.for manpage in ${MAN1} + @ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/ +.endfor +.if !defined(NOPORTDOCS) + @ ${MKDIR} ${FASTA3_DOCDIR} +.for docfile in ${FASTA3_DOCS} + @ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR} +.endfor +.endif +.if !defined(BATCH) + @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' pkg-message > ${PKGMESSAGE} + @ ${CAT} ${PKGMESSAGE} +.endif + +.include <bsd.port.mk> diff --git a/biology/fasta3/distinfo b/biology/fasta3/distinfo new file mode 100644 index 000000000000..d04229bf215c --- /dev/null +++ b/biology/fasta3/distinfo @@ -0,0 +1 @@ +MD5 (fasta33t08.shar.Z) = 94f702aa1e9e25c44806088ff6871409 diff --git a/biology/fasta3/files/patch-Makefile b/biology/fasta3/files/patch-Makefile new file mode 100644 index 000000000000..bdc135f01c97 --- /dev/null +++ b/biology/fasta3/files/patch-Makefile @@ -0,0 +1,49 @@ +--- Makefile.orig Mon Jan 29 13:44:28 2001 ++++ Makefile Mon Jan 29 14:08:43 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 + # + # 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 ++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 + # -I/usr/local/include/mysql -DMYSQL_DB + #(for mySQL databases) (also requires change to Makefile33.common) + +@@ -32,11 +32,15 @@ + HFLAGS= -o + NFLAGS= -o + +-#for DEC Unix V4.0 + THR_SUBS = pthr_subs +-THR_LIBS = -threads ++THR_LIBS = -pthread + 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 = ${PREFIX}/bin + + # renamed (fasta33) programs +-include Makefile33.common ++# include Makefile33.common + # conventional (fasta3) names +-#include Makefile.common ++include Makefile.common diff --git a/biology/fasta3/files/patch-Makefile.common b/biology/fasta3/files/patch-Makefile.common new file mode 100644 index 000000000000..395da695e031 --- /dev/null +++ b/biology/fasta3/files/patch-Makefile.common @@ -0,0 +1,20 @@ +--- 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 --git a/biology/fasta3/pkg-comment b/biology/fasta3/pkg-comment new file mode 100644 index 000000000000..42bea2b9a553 --- /dev/null +++ b/biology/fasta3/pkg-comment @@ -0,0 +1 @@ +A collection of programs for searching DNA and protein databases, V 3 diff --git a/biology/fasta3/pkg-descr b/biology/fasta3/pkg-descr new file mode 100644 index 000000000000..9aac7813aa95 --- /dev/null +++ b/biology/fasta3/pkg-descr @@ -0,0 +1,20 @@ +Version 3 of the FASTA packages contains many programs for searching DNA and +protein databases and one program (prss3) for evaluating statistical +significance from randomly shuffled sequences. Several additional analysis +programs, including programs that produce local alignments, are available as +part of version 2 of the FASTA package, which is available as the port +biology/fasta. + +FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved +Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson +(1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; +Pearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in +Molecular Biology 132:185-219. + +The FASTA3 suite is distributed freely subject to the condition that it may +not be sold or incorporated into a commercial product. + +Author: William R Pearson <wrp@virginia.edu> +WWW: http://fasta.bioch.virginia.edu/ + +-- Johann Visagie <johann@egenetics.com> diff --git a/biology/fasta3/pkg-message b/biology/fasta3/pkg-message new file mode 100644 index 000000000000..4a6cc7e32515 --- /dev/null +++ b/biology/fasta3/pkg-message @@ -0,0 +1,15 @@ +-------------------------------------------------------------------------- + +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 --git a/biology/fasta3/pkg-plist b/biology/fasta3/pkg-plist new file mode 100644 index 000000000000..a73cd6e197a8 --- /dev/null +++ b/biology/fasta3/pkg-plist @@ -0,0 +1,45 @@ +%%PORTDOCS%%share/doc/fasta3/00README.1st +%%PORTDOCS%%share/doc/fasta3/COPYRIGHT +%%PORTDOCS%%share/doc/fasta3/README +%%PORTDOCS%%share/doc/fasta3/fasta3x.doc +%%PORTDOCS%%share/doc/fasta3/fasta3x.me +%%PORTDOCS%%share/doc/fasta3/readme.mpi_3.3 +%%PORTDOCS%%share/doc/fasta3/readme.pvm_2.0 +%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.0 +%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.2 +%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.3 +%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.4 +%%PORTDOCS%%share/doc/fasta3/readme.v30 +%%PORTDOCS%%share/doc/fasta3/readme.v30t6 +%%PORTDOCS%%share/doc/fasta3/readme.v30t7 +%%PORTDOCS%%share/doc/fasta3/readme.v31t0 +%%PORTDOCS%%share/doc/fasta3/readme.v31t1 +%%PORTDOCS%%share/doc/fasta3/readme.v32t0 +%%PORTDOCS%%share/doc/fasta3/readme.v33t0 +%%PORTDOCS%%share/doc/fasta3/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%%@dirrm share/doc/fasta3 |