Bug 78963 - [maintainer update] update biology/blast
Summary: [maintainer update] update biology/blast
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: freebsd-ports-bugs mailing list
Depends on:
Reported: 2005-03-17 21:50 UTC by Fernan Aguero
Modified: 2005-03-18 13:01 UTC (History)
0 users

See Also:

blast.diff (2.03 KB, patch)
2005-03-17 21:50 UTC, Fernan Aguero
no flags Details | Diff

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Description Fernan Aguero 2005-03-17 21:50:02 UTC
	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

	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.
Comment 1 Alexey Dokuchaev freebsd_committer 2005-03-18 13:01:14 UTC
State Changed
From-To: open->closed

Committed, thanks!