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New port: biology/fasta, the FASTA2 suite of DNA and protein sequence
search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com>
This commit is contained in:
parent
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Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=38205
@ -7,6 +7,7 @@
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SUBDIR += clustalw
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SUBDIR += deft
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SUBDIR += emboss
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SUBDIR += fasta
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SUBDIR += fastdnaml
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SUBDIR += gaussian98
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SUBDIR += gperiodic
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47
biology/fasta/Makefile
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47
biology/fasta/Makefile
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@ -0,0 +1,47 @@
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# New ports collection makefile for: fasta
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# Date created: 29 January 2001
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# Whom: Johann Visagie <johann@egenetics.com>
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#
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# $FreeBSD$
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#
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PORTNAME= fasta
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PORTVERSION= 20.u66
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CATEGORIES= biology
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MASTER_SITES= http://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= johann@egenetics.com
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NO_CDROM= May not be sold or incorporated into a commercial product
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WRKSRC= ${WRKDIR}/fasta
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PKGMESSAGE= ${WRKDIR}/pkg-message
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FASTA_DOCDIR= ${PREFIX}/share/doc/fasta
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FASTA_DOCS= COPYRIGHT README.versions fasta20.doc fasta20.me format.doc \
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readme.*
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MAN1= align.1 fasta.1 lalign.1 prdf.1 prss.1 randseq.1 ssearch.1
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MLINKS= fasta.1 tfasta.1 fasta.1 lfasta.1 fasta.1 plfasta.1 \
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fasta.1 fastx.1 fasta.1 tfastx.1 \
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align.1 align0.1 lalign.1 plalign.1
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do-extract:
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@ ${RM} -rf ${WRKDIR}
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@ ${MKDIR} ${WRKSRC}
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@ for file in ${EXTRACT_ONLY}; do \
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cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \
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done
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post-install:
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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} ${FASTA_DOCDIR}
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.for docfile in ${FASTA_DOCS}
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@ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${FASTA_DOCDIR}
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.endfor
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.endif
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.include <bsd.port.mk>
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1
biology/fasta/distinfo
Normal file
1
biology/fasta/distinfo
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MD5 (fasta20u66.shar.Z) = 3960df040e5006969cf02568544751e9
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28
biology/fasta/files/patch-Makefile
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28
biology/fasta/files/patch-Makefile
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@ -0,0 +1,28 @@
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--- Makefile.orig Mon Jan 29 15:10:42 2001
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+++ Makefile Mon Jan 29 15:15:08 2001
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@@ -3,13 +3,13 @@
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# for mips, also use: -mips2 -O2
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#
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-CC= cc -O
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+#CC= cc -O
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#CC=cc -g
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-CFLAGS= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS
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+CFLAGS+= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS
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LFLAGS= -lm -o
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-BIN = /seqprg/slib/bin
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+BIN = $(PREFIX)/bin
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#NRAND= nrand
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#IBM RS/6000
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NRAND= nrand48
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@@ -29,7 +29,7 @@
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sall : $(SPROGS)
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install :
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- cp $(PROGS) $(BIN)
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+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(BIN)
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clean-up :
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rm *.o $(PROGS)
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1
biology/fasta/pkg-comment
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1
biology/fasta/pkg-comment
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A collection of programs for searching DNA and protein databases
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biology/fasta/pkg-descr
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biology/fasta/pkg-descr
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Version 2 of the FASTA packages contains many programs for searching DNA and
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protein databases, performing sequence comparisons, producing local
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alignments, and other related tasks.
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Currently, the FASTA2 suite is in maintenance mode. Updated versions of ONLY
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the searching programs are available in version 3 of the FASTA packages,
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which may be found in the port biology/fasta3.
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FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved
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Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R.
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Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA"
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Methods in Enzymology 183:63- 98).
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The FASTA2 suite is distributed freely subject to the condition that it may
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not be sold or incorporated into a commercial product.
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Author: William R Pearson <wrp@virginia.edu>
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WWW: http://fasta.bioch.virginia.edu/
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-- Johann Visagie <johann@egenetics.com>
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15
biology/fasta/pkg-message
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15
biology/fasta/pkg-message
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--------------------------------------------------------------------------
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The FASTA3 package has been successfully installed.
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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
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to suit the requirements of a particular site.
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In order to use the FASTA3 programs, a user must set the environment
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variable FASTLIBS to contain the full path of the FASTA3 configuration
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file, e.g.:
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- set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
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--------------------------------------------------------------------------
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38
biology/fasta/pkg-plist
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38
biology/fasta/pkg-plist
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%%PORTDOCS%%share/doc/fasta/COPYRIGHT
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%%PORTDOCS%%share/doc/fasta/README.versions
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%%PORTDOCS%%share/doc/fasta/fasta20.doc
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%%PORTDOCS%%share/doc/fasta/fasta20.me
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%%PORTDOCS%%share/doc/fasta/format.doc
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%%PORTDOCS%%share/doc/fasta/readme.v15
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%%PORTDOCS%%share/doc/fasta/readme.v16
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%%PORTDOCS%%share/doc/fasta/readme.v17
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%%PORTDOCS%%share/doc/fasta/readme.v20
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%%PORTDOCS%%share/doc/fasta/readme.v20u4
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%%PORTDOCS%%share/doc/fasta/readme.v20u5
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%%PORTDOCS%%share/doc/fasta/readme.v20u6
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bin/aacomp
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bin/align
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bin/align0
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bin/bestscor
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bin/crandseq
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bin/fasta
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bin/fastx
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bin/flalign
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bin/fromgb
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bin/garnier
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bin/grease
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bin/lalign
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bin/lfasta
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bin/plalign
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bin/plfasta
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bin/prdf
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bin/prss
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bin/psgrease
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bin/randseq
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bin/relate
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bin/ssearch
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bin/tfasta
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bin/tfastx
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bin/tgrease
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bin/zs_exp
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%%PORTDOCS%%@dirrm share/doc/fasta
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