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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>. -.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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
