Date: Thu, 17 Mar 2005 18:45:49 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/78963: [maintainer update] update biology/blast Message-ID: <200503172145.j2HLjn4V053261@pi.iib.unsam.edu.ar> Resent-Message-ID: <200503172150.j2HLo2oL006212@freefall.freebsd.org>
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>Number: 78963 >Category: ports >Synopsis: [maintainer update] update biology/blast >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Thu Mar 17 21:50:02 GMT 2005 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 4.10-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan@pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386 >Description: I've added PORTREVISION to the port and set it to the release date as in the lang/gcc* ports. Since the distinfo file is not used, this would help users know when they have to update their ports. Although newer release might be made, the idea is to bump PORTREVISION for important feature releases on when significant bugs are fixed. Other minor (cosmetic) changes also applied. From the release notes: The [16-Mar-2005] release of WU BLAST 2.0 has been posted. This is principally a new feature release. Parameter descriptions have been updated on-line at http://blast.wustl.edu/blast/parameters.html The new features include: o Multiple output formats are now supported by the search programs and are selectable through the new "mformat" parameter. Tabular output (mformat=2 or mformat=3) is the notable addition. o An alternative, single-line format for NOTE, WARNING, ERROR and FATAL messages can be selected with the new "msgstyle" parameter (msgstyle=1). The single-line format also includes the identifier of the current query sequence. o BLASTX and TBLASTX searches can be restricted to a single reading frame of the query sequence, with the new "qframe" parameter. o An alternative report format from the xdformat and xdget programs can be selected with the new -m parameter. When dumping or retrieving sequences and -m1 is specified, just the sequence identifiers and their associated sequence lengths are reported. In the area of bug fixes, perhaps the most important change is: o Consistency is uniformly enforced between the score thresholds S, S2 and gapS2. The software now reduces S2 and gapS2 if necessary to maintain the relationship S >= gapS2 >= S2. A WARNING is emitted if the original, higher value for S2 or gapS2 was explicitly set on the command line or indirectly set via the E2 or gapE2 command line parameters. >How-To-Repeat: >Fix: --- blast.diff begins here --- diff -ruN /usr/ports/biology/blast/Makefile blast/Makefile --- /usr/ports/biology/blast/Makefile Fri Nov 19 14:27:44 2004 +++ blast/Makefile Thu Mar 17 16:58:44 2005 @@ -1,3 +1,4 @@ +# ex:ts=8 # New ports collection makefile for: WU BLAST # Date created: 27 May 2004 # Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> @@ -7,6 +8,7 @@ PORTNAME= wu-blast PORTVERSION= 2.0 +PORTREVISION= 20050316 CATEGORIES= biology MASTER_SITES= # EXTRACT_SUFX= .tar.Z @@ -14,7 +16,8 @@ MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= WU BLAST, a software package for sequence similarity searches -# Distfiles change every few days +# Distfiles change rapidly, but since they can only be downloaded from +# the author, this is not a problem. IGNOREFILES= ${DISTFILES} RESTRICTED= "License does not allow redistribution of binaries. You should first register for the software, which is free for academic use." @@ -27,7 +30,7 @@ PKGMESSAGE= ${WRKDIR}/pkg-message PORTDOCS= COPYRIGHT FAQ-Indexing.html HISTORY LICENSE Memory.html \ - README.html parameters.html + README.html parameters.html parameters.pdf BINS= blasta gb2fasta gt2fasta memfile nrdb pam patdb \ pir2fasta sp2fasta xdformat xdget SCRIPTS= wu-blastall wu-formatdb diff -ruN /usr/ports/biology/blast/pkg-plist blast/pkg-plist --- /usr/ports/biology/blast/pkg-plist Thu Nov 11 18:35:03 2004 +++ blast/pkg-plist Thu Mar 17 16:45:42 2005 @@ -18,6 +18,14 @@ bin/tblastx bin/setdb bin/pressdb +%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT +%%PORTDOCS%%%%DOCSDIR%%/FAQ-Indexing.html +%%PORTDOCS%%%%DOCSDIR%%/HISTORY +%%PORTDOCS%%%%DOCSDIR%%/LICENSE +%%PORTDOCS%%%%DOCSDIR%%/Memory.html +%%PORTDOCS%%%%DOCSDIR%%/README.html +%%PORTDOCS%%%%DOCSDIR%%/parameters.html +%%PORTDOCS%%%%DOCSDIR%%/parameters.pdf %%DATADIR%%/matrix/aa/nuc.4.4 %%DATADIR%%/matrix/aa/BLOSUM30 %%DATADIR%%/matrix/aa/BLOSUM35 @@ -202,6 +210,7 @@ %%DATADIR%%/filter/pseg %%DATADIR%%/filter/README %%DATADIR%%/sysblast.sample +%%PORTDOCS%%@dirrm %%DOCSDIR%% @dirrm %%DATADIR%%/matrix/aa @dirrm %%DATADIR%%/matrix/nt @dirrm %%DATADIR%%/matrix --- blast.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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