ports/78963: [maintainer update] update biology/blast
Fernan Aguero
fernan at iib.unsam.edu.ar
Thu Mar 17 21:50:05 UTC 2005
>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 at 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 at 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 at 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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