Date: Mon, 20 Mar 2006 13:49:01 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/94741: [ maintainer update ] update biology/fasta3 Message-ID: <200603201649.k2KGn1WF003813@omega.iib.unsam.edu.ar> Resent-Message-ID: <200603201700.k2KH0cZg011553@freefall.freebsd.org>
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>Number: 94741
>Category: ports
>Synopsis: [ maintainer update ] update biology/fasta3
>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: Mon Mar 20 17:00:38 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD 6.0-RELEASE-p4 i386
>Organization:
IIB-UNSAM
>Environment:
System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386
>Description:
A new version of the fasta distribution, fasta34t25d5.shar.Z, is
available from:
ftp://ftp.virginia.edu/pub/fasta/fasta34t25d5.shar.Z
In general, the major changes in this version are internal; the
functions producing alignments and alignment coordinates have been
simplified. One of the consequences is that for the parallel
versions, alignments are calculated only once, even if the alignment
information is needed several times (e.g. in the list of best scores
and as final alignments).
The major new feature is the ability to work with asymmetric scoring matrices.
Although the FASTA programs use the NxN scoring matrix format used by BLAST,
only half of the matrix was actually read andthe rest inferred by symmetry.
This has been changed, and asymmetric matrices can be used.
In addition, the -V "*#" annotation option is now available in the
parallel versions of the programs, and some minor bug fixes are
included.
Bill Pearson
>How-To-Repeat:
>Fix:
--- fasta3.diff begins here ---
diff -u /usr/ports/biology/fasta3/Makefile fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile Wed Mar 1 20:11:41 2006
+++ fasta3/Makefile Mon Mar 20 13:38:06 2006
@@ -7,7 +7,7 @@
#
PORTNAME= fasta3
-PORTVERSION= 34.t25.d4
+PORTVERSION= 34.t25.d5
CATEGORIES= biology
MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/
DISTNAME= fasta${PORTVERSION:S/.//g}
diff -u /usr/ports/biology/fasta3/distinfo fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo Wed Mar 1 20:11:41 2006
+++ fasta3/distinfo Mon Mar 20 13:38:09 2006
@@ -1,3 +1,3 @@
-MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7
-SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe
-SIZE (fasta34t25d4.shar.Z) = 799416
+MD5 (fasta34t25d5.shar.Z) = 500a449fe3eeebbeb3e7f53f652505c7
+SHA256 (fasta34t25d5.shar.Z) = bcb7c25b6e3d883cc4c61c35b94b4dc42c49a158859cfefbf6a3f9357c0e7482
+SIZE (fasta34t25d5.shar.Z) = 795675
Common subdirectories: /usr/ports/biology/fasta3/files and fasta3/files
--- fasta3.diff ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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