[med-svn] r6712 - trunk/packages/ncbi-blast-plus/trunk/debian

[olivier sallou]

Author: osallou-guest
Date: 2011-04-29 07:54:30 +0000 (Fri, 29 Apr 2011)
New Revision: 6712

Added:
   trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1
   trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages
Removed:
   trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.doc-base.EX
Log:
update doc

Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1	                        (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1	2011-04-29 07:54:30 UTC (rev 6712)
@@ -0,0 +1,33 @@
+.TH ncbi-blast-plus 1  "April 29, 2011" "version 2.2.25" "USER COMMANDS"
+.SH NAME
+ncbi-blast-plus \- NCBI command tools for BLAST+
+.SH ONELINE DOCUMENTATION
+.B BLAST+ documentation is available online at http://www.ncbi.nlm.nih.gov/books/NBK1763/
+.PP
+.SH DESCRIPTION
+The NCBI BLAST+ is a group of tools for basic alignment search. BLAST+
+ is a rewrite of BLAST with new features and performance improvements.
+BLAST+ commands differ from original BLAST. For BLAST users, one should read
+ the BLAST USERS paragraph.
+.PP
+.SH CONFIGURATION
+BLAST+ uses the BLASTDB environment variable to get default db directory.
+It is possible to update the file /etc/ncbi/.ncbirc to add the following:
+.B [BLAST]
+.B BLASTDB=/var/lib/ncbi-blast-plus/db
+.SH BLAST USERS
+The easiest way to get started using these command line applications is
+ by means of the legacy_blast.pl PERL script which is bundled along with
+ the BLAST+ applications.
+To utilize this script, simply prefix it to the invocation of the C toolkit
+ BLAST command line application and append the --path option pointing to the 
+installation directory of the BLAST+ applications. For example, instead of using
+
+.B blastall -i query -d nr -o blast.out 
+use
+.B legacy_blast.pl blastall -i query -d nr -o blast.out --path /usr/bin
+
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+NCBI - BLAST+

Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.doc-base.EX
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.doc-base.EX	2011-04-29 07:43:26 UTC (rev 6711)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.doc-base.EX	2011-04-29 07:54:30 UTC (rev 6712)
@@ -1,20 +0,0 @@
-Document: ncbi-blast-plus
-Title: Debian ncbi-blast-plus Manual
-Author: <insert document author here>
-Abstract: This manual describes what ncbi-blast-plus is
- and how it can be used to
- manage online manuals on Debian systems.
-Section: unknown
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/ncbi-blast-plus/ncbi-blast-plus.sgml.gz
-
-Format: postscript
-Files: /usr/share/doc/ncbi-blast-plus/ncbi-blast-plus.ps.gz
-
-Format: text
-Files: /usr/share/doc/ncbi-blast-plus/ncbi-blast-plus.text.gz
-
-Format: HTML
-Index: /usr/share/doc/ncbi-blast-plus/html/index.html
-Files: /usr/share/doc/ncbi-blast-plus/html/*.html

Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages	                        (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages	2011-04-29 07:54:30 UTC (rev 6712)
@@ -0,0 +1 @@
+debian/*.1