[med-svn] [gmap] 03/03: d/manpages: install gmap_build d/copyright: included full text of BSD license d/gmap_setup.1: binary is deprecated and removed from the distribution
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Thu Jul 3 15:25:25 UTC 2014
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 493c3111801f364b5b28368fbe7460f76d874a20
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Thu Jul 3 17:12:54 2014 +0200
d/manpages: install gmap_build
d/copyright: included full text of BSD license
d/gmap_setup.1: binary is deprecated and removed from the distribution
---
debian/copyright | 33 ++++++++++++++++-
debian/gmap_setup.1 | 102 ----------------------------------------------------
debian/manpages | 2 +-
3 files changed, 33 insertions(+), 104 deletions(-)
diff --git a/debian/copyright b/debian/copyright
index 3397e8f..4c7d8cf 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -71,7 +71,38 @@ License: MIT
Files: src/fastlog.h
Copyright: 2012 Paul Mineiro <paul at mineiro.com>
License: BSD
- See `/usr/share/common-licenses/BSD'.
+ Redistribution and use in source and binary forms, with
+ or without modification, are permitted provided that the
+ following conditions are met:
+ .
+ * Redistributions of source code must retain the
+ above copyright notice, this list of conditions and
+ the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the
+ above copyright notice, this list of conditions and
+ the following disclaimer in the documentation and/or
+ other materials provided with the distribution.
+ .
+ * Neither the name of Paul Mineiro nor the names
+ of other contributors may be used to endorse or promote
+ products derived from this software without specific
+ prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+ GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
Files: debian/*
Copyright: 2011 Shaun Jackman <sjackman at debian.org>
diff --git a/debian/gmap_setup.1 b/debian/gmap_setup.1
deleted file mode 100644
index aab9a93..0000000
--- a/debian/gmap_setup.1
+++ /dev/null
@@ -1,102 +0,0 @@
-.TH GMAP_SETUP "1" "Nov 2011" "GMAP 2011-11-30" "User Commands"
-.SH NAME
-gmap_setup \- create a genome database for GMAP or GSNAP
-.SH SYNOPSIS
-.B gmap_setup
-\fB-d\fR\fIgenomename\fR [\fB-D\fR\fIdestdir\fR]
-[\fB-o\fR\fIMakefile\fR] \fIFASTA\fR
-.SH OPTIONS
-.TP
-\fB\-d\fR
-genome name
-.TP
-\fB\-D\fR
-destination directory for installation (defaults to gmapdb directory specified at configure time)
-.TP
-\fB\-o\fR
-name of output Makefile (default is "Makefile.<genome>")
-.TP
-\fB\-M\fR
-use coordinates from an .md file (e.g., seq_contig.md file from NCBI)
-.TP
-\fB\-C\fR
-try to parse chromosomal coordinates from each FASTA header
-.TP
-\fB\-E\fR
-interpret argument as a command, instead of a list of FASTA files
-.TP
-\fB\-O\fR
-order chromosomes in numeric/alphabetic order (0 = no, 1 = yes (default))
-.SS Advanced options
-.TP
-\fB\-W\fR
-write some output directly to file, instead of using RAM (use only if RAM is limited)
-.TP
-\fB\-q\fR
-GMAP indexing interval (default: 3 nt)
-.TP
-\fB\-Q\fR
-PMAP indexing interval (default: 6 aa)
-.SH DESCRIPTION
-.PP
-If you want to treat each FASTA entry as a separate chromosome (either
-because it is in fact an entire chromosome or because you have contigs
-without any chromosomal information), you can simply call gmap_setup
-like this:
-.IP
-gmap_setup \fB\-d\fR <genome> <fasta_file>...
-.PP
-The accession of each FASTA header (the word following each ">") will
-be the name of each chromosome. GMAP can handle an unlimited number
-of "chromosomes", with arbitrarily long names. In this way, GMAP
-could be used as a general search program for near\-identity matches
-against a FASTA file.
-.TP
-\fB\-M\fR and \fB\-C\fR
-If your sequences represent contigs that have
-mapping information to specific chromosomal regions, then you can
-have gmap_setup try to read each header to determine its chromosomal
-region (the \fB\-C\fR flag) or read an .md file that contains information
-about chromosomal regions (the \fB\-M\fR flag). The .md files are often
-provided in NCBI releases, but since the formats change often,
-gmap_setup will prompt you to make sure it parses it correctly.
-.TP
-\fB\-E\fR
-If you need to pre\-process the FASTA files before using
-these programs, perhaps because they are compressed or because you
-need to insert chromosomal information in the header lines, you can
-specify a command instead of multiple fasta_files, like these
-examples:
-
- gmap_setup \fB\-d\fR <genome> \fB\-E\fR 'gunzip \fB\-c\fR genomefiles.gz'
- gmap_setup \fB\-d\fR <genome> \fB\-E\fR 'cat *.fa | ./add\-chromosomal\-info.pl'
-.TP
-\fB\-W\fR
-The gmap_setup process works best if you have a
-computer with enough RAM to hold the entire genome (e.g., 3
-gigabytes for a human\- or mouse\-sized genome). Since the resulting
-genome files work across all machine architectures, you can find any
-machine with sufficient RAM to build the genome files and then
-transfer the files to another machine. (GMAP itself runs fine on
-machines with limited RAM.) If you cannot find any machine with
-sufficient RAM for gmap_setup, you can run the program with the \fB\-W\fR
-flag to write the files directly, but this can be very slow.
-.TP
-\fB\-q\fR and \fB\-Q\fR
-If you specify a smaller interval (for example,
-3 for the GMAP interval), you can create a higher\-resolution
-database, which can be useful for mapping small oligomers (smaller
-than 18 nt). However, the corresponding genome index files will be
-larger (twice as big if you specify \fB\-q\fR 3). These index files may
-exceed the 2 gigabyte file offset limit on some computers, and will
-therefore fail to work on those computers.
-.SH AUTHOR
-Thomas D. Wu and Colin K. Watanabe
-.SH "REPORTING BUGS"
-Report bugs to Thomas Wu <twu at gene.com>.
-.SH COPYRIGHT
-Copyright 2005 Genentech, Inc. All rights reserved.
-.SH "SEE ALSO"
-\fBgmap\fR(1), \fBgsnap\fR(1)
-.br
-http://research-pub.gene.com/gmap/
diff --git a/debian/manpages b/debian/manpages
index 5ba1fda..75e8123 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1,3 +1,3 @@
debian/gmap.1
-debian/gmap_setup.1
+debian/gmap_build.1
debian/gsnap.1
--
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