Date: Mon, 29 Jun 1998 17:31:18 -0500 (CDT) From: barnhart@sequencer.wustl.edu To: FreeBSD-gnats-submit@FreeBSD.ORG Subject: ports/7120: New port: biology/hmmer Message-ID: <199806292231.RAA00305@polvo.wustl.edu>
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>Number: 7120 >Category: ports >Synopsis: New port: biology/hmmer >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: sw-bug >Submitter-Id: current-users >Arrival-Date: Mon Jun 29 15:40:01 PDT 1998 >Last-Modified: >Originator: Matthew Jason Euclid Barnhart >Organization: Washington University School of Medicine, Department of Genetics >Release: FreeBSD 3.0-CURRENT i386 >Environment: >Description: Output of shar `find hmmer` for new Port, hmmer. >How-To-Repeat: >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # hmmer # hmmer/files # hmmer/files/md5 # hmmer/patches # hmmer/patches/patch-aa # hmmer/patches/patch-ab # hmmer/pkg # hmmer/pkg/COMMENT # hmmer/pkg/DESCR # hmmer/pkg/MESSAGE # hmmer/pkg/PLIST # hmmer/Makefile # echo c - hmmer mkdir -p hmmer > /dev/null 2>&1 echo c - hmmer/files mkdir -p hmmer/files > /dev/null 2>&1 echo x - hmmer/files/md5 sed 's/^X//' >hmmer/files/md5 << 'END-of-hmmer/files/md5' XMD5 (hmmer-2.0.tar.Z) = 7e993a3883046840f0672ea004bc268b END-of-hmmer/files/md5 echo c - hmmer/patches mkdir -p hmmer/patches > /dev/null 2>&1 echo x - hmmer/patches/patch-aa sed 's/^X//' >hmmer/patches/patch-aa << 'END-of-hmmer/patches/patch-aa' X*** Makefile.DIST Mon Jun 29 12:22:00 1998 X--- Makefile Mon Jun 29 15:44:00 1998 X*************** X*** 22,29 **** X # where you want things installed X # Many installations will want to change $(HOME) to /usr/local, for instance X # X! BINDIR = $(HOME)/bin X! MANDIR = $(HOME)/man X X # your compiler and compiler flags X # X--- 22,29 ---- X # where you want things installed X # Many installations will want to change $(HOME) to /usr/local, for instance X # X! BINDIR = /usr/local/bin X! MANDIR = /usr/local/man X X # your compiler and compiler flags X # END-of-hmmer/patches/patch-aa echo x - hmmer/patches/patch-ab sed 's/^X//' >hmmer/patches/patch-ab << 'END-of-hmmer/patches/patch-ab' X*** Shiva/Makefile.DIST Mon Jun 29 16:38:26 1998 X--- Shiva/Makefile Mon Jun 29 16:38:45 1998 X*************** X*** 75,81 **** X echo $$shivatest: ok;\ X done X @echo Scripted Shiva tests: X! ./Optiontests.pl X X ####### X ## Miscellaneous X--- 75,81 ---- X echo $$shivatest: ok;\ X done X @echo Scripted Shiva tests: X! perl Optiontests.pl X X ####### X ## Miscellaneous END-of-hmmer/patches/patch-ab echo c - hmmer/pkg mkdir -p hmmer/pkg > /dev/null 2>&1 echo x - hmmer/pkg/COMMENT sed 's/^X//' >hmmer/pkg/COMMENT << 'END-of-hmmer/pkg/COMMENT' XProfile hidden Markov models for biological sequence analysis. END-of-hmmer/pkg/COMMENT echo x - hmmer/pkg/DESCR sed 's/^X//' >hmmer/pkg/DESCR << 'END-of-hmmer/pkg/DESCR' XHMMER is an implementation of profile HMM methods for sensitive database Xsearches using multiple sequence alignments as queries. X XBasically, you give HMMER a multiple sequence alignment as input; it builds Xa statistical model called a "hidden Markov model" which you can then use as Xa query into a sequence database to find (and/or align) additional Xhomologues of the sequence family. X XHmmer is developed by Sean Eddy at Washington University School of Medicine. XMore information is available at http://hmmer.wustl.edu/ END-of-hmmer/pkg/DESCR echo x - hmmer/pkg/MESSAGE sed 's/^X//' >hmmer/pkg/MESSAGE << 'END-of-hmmer/pkg/MESSAGE' X********************************************************* X XNote on environment variables: X X HMMER reads three environment variables: X HMMERDB - directory location of HMM databases (e.g. PFAM) X BLASTDB - directory location of FASTA-formatted sequence databases X BLASTMAT - directory location of PAM scoring matrices X X If you have installed BLAST, you probably already have these X environment variables set in system-wide or user-specific X .cshrc files. They are optional. If they are set up, you X can simplify command lines to: X > hmmpfam pfam my.query X > hmmsearch my.hmm swiss35 X instead of X > hmmpfam /some/long/path/to/databases/pfam my.query X > hmmsearch my.hmm /some/long/path/to/databases/swiss35 X XPlease see the website http://hmmer.wustl.edu/ for more information. X X********************************************************* END-of-hmmer/pkg/MESSAGE echo x - hmmer/pkg/PLIST sed 's/^X//' >hmmer/pkg/PLIST << 'END-of-hmmer/pkg/PLIST' Xbin/hmmalign Xbin/hmmbuild Xbin/hmmcalibrate Xbin/hmmconvert Xbin/hmmemit Xbin/hmmpfam Xbin/hmmsearch Xman/man1/hmmalign.1.gz Xman/man1/hmmbuild.1.gz Xman/man1/hmmcalibrate.1.gz Xman/man1/hmmconvert.1.gz Xman/man1/hmmemit.1.gz Xman/man1/hmmer.1.gz Xman/man1/hmmpfam.1.gz Xman/man1/hmmsearch.1.gz Xshare/doc/hmmer/Userguide.ps END-of-hmmer/pkg/PLIST echo x - hmmer/Makefile sed 's/^X//' >hmmer/Makefile << 'END-of-hmmer/Makefile' X# New ports collection Makefile for: hmmer X# Version required: 2.0 X# Date created: June 29 1998 X# Whom: barnhart@genetics.wustl.edu X# X# $Id$ X# X XDISTNAME= hmmer-2.0 XCATEGORIES= biology XMASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/ XEXTRACT_SUFX= .tar.Z X XMAINTAINER= barnhart@genetics.wustl.edu X XBUILD_DEPENDS= perl:${PORTSDIR}/lang/perl5 X XMAN1= hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 hmmer.1 hmmpfam.1 hmmsearch.1 X XWRKSRC= ${WRKDIR}/build/${DISTNAME} X Xpost-build: X @ strip ${WRKSRC}/binaries/* X @ make test X Xtest: X @(cd ${WRKSRC}; make test) X Xpost-install: X.if !defined(NOPORTDOCS) X ${MKDIR} ${PREFIX}/share/doc/hmmer X ${INSTALL_MAN} ${WRKSRC}/Userguide/Userguide.ps ${PREFIX}/share/doc/hmmer X.endif X @ ${CAT} ${PKGDIR}/MESSAGE X X.include <bsd.port.mk> END-of-hmmer/Makefile exit >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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