Author: tille Date: 2014-01-08 18:33:08 +0000 (Wed, 08 Jan 2014) New Revision: 15732
Added: trunk/packages/anfo/trunk/debian/anfo.1 trunk/packages/anfo/trunk/debian/anfo.manpages trunk/packages/anfo/trunk/debian/upstream Modified: trunk/packages/anfo/trunk/debian/changelog trunk/packages/anfo/trunk/debian/rules Log: ack for BioLinux changes; add manpage from upstream repository; add link to upstream repository Added: trunk/packages/anfo/trunk/debian/anfo.1 =================================================================== --- trunk/packages/anfo/trunk/debian/anfo.1 (rev 0) +++ trunk/packages/anfo/trunk/debian/anfo.1 2014-01-08 18:33:08 UTC (rev 15732) @@ -0,0 +1,127 @@ +.\" https://raw.github.com/udo-stenzel/anfo/master/man/anfo.1 +.\" ANFO short read aligner +.\" (C) 2009 Udo Stenzel +.\" +.\" This program is free software; you can redistribute it and/or modify +.\" it under the terms of the GNU General Public License as published by +.\" the Free Software Foundation; either version 3 of the License, or (at +.\" your option) any later version. See the COPYING file for details. + +.\" Process this file with +.\" groff -man -Tascii patman.1 +.\" +.TH ANFO 1 "OCTOBER 2009" Applications "User Manuals" +.SH NAME +anfo \- find best alignment of short reads to database +.SH SYNOPSIS +.B anfo [ +.I option +.B | +.I file +.B ... ] +.SH DESCRIPTION +.B anfo +aligns (short) sequencing reads to a (gigabase sized) database. It uses +a heuristic seeding method, but then applies a genuine aligner that +allows gaps, understands damage patterns in ancient dna and produces an +easy to interpret score. + +Input files can be any variety of FastA or FastQ files, or a native +.B anfo +binary file, optinally compressed using +.BR gzip or bzip2 . +The file format is automatically recognized and other formats may be +added. + + +.SH OPTIONS +.IP "-V, --version" +Print version number and exit. + +.IP "-o file, --output file" +Write output to +.IR file ". " file +will be written in the native +.B anfo +binary format, which can be operated upon using +.B anfo-tool +or the bindings to +.BR guile . + +.IP "-c conffile, --config conffile" +Read configuration from +.IR conffile . +This file configures which indices are used, and by extension to which +genomes an alignment is made, what parameters to use in the aligner and +can set paths. See the example file. + +.IP "-p num, --threads num" +Start +.I num +threads for alignment. One such thread per processor core is usually +best. + +.IP "-x num, --ixthreads num" +Start +.I num +threads for indexing. Indexing normally uses less cpu power than +alignment, so fewer indexers than aligners is normally best. + +.IP "--solexa-scale" +When reading FastQ files, use the Solexa scale (log-odds-ratios) instead +of the standard Phread scale (probabilities). If you use +Solexa/Illumina sequencers, refer to your documentation whether you need +this. Else you don't. + +.IP "--fastq-origin ori" +Set origin for FastQ decoding to +.IR ori . +The standard and default is 33, but it must be set to 64 for some +versions of the Solexa/Illumina software. If you use Solexa/Illumina +sequencers, refer to your documentation whether you need this. Else you +don't. + +.IP "-q, --quiet" +Suppress all output except fatal errors. + +.IP "-v, --verbose" +Print a progress indicator during operation. + + +.SH ENVIRONMENT +.IP ANFO_PATH +Colon separated list of directories searched for genome and index files. + +.SH FILES +.I /etc/popt +.RS +The system wide configuration file for +.BR popt (3). +.B anfo +identifies itself as "anfo" to popt. +.RE + +.I ~/.popt +.RS +Per user configuration file for +.BR popt (3). +.RE + +.I /usr/share/doc/anfo/example/*.cfg +.RS +Example configuration files to be used with +.BR anfo . +.RE + +.SH BUGS +None known. + +.SH AUTHOR +Udo Stenzel <[email protected]> + +.SH "SEE ALSO" +http://bioinf.eva.mpg.de/anfo + +.BR anfo-tool "(1), " anfo-sge "(1), " fa2dna "(1), " dnaindex "(1), " popt "(3), " fasta (5) + + Added: trunk/packages/anfo/trunk/debian/anfo.manpages =================================================================== --- trunk/packages/anfo/trunk/debian/anfo.manpages (rev 0) +++ trunk/packages/anfo/trunk/debian/anfo.manpages 2014-01-08 18:33:08 UTC (rev 15732) @@ -0,0 +1 @@ +debian/*.1 Modified: trunk/packages/anfo/trunk/debian/changelog =================================================================== --- trunk/packages/anfo/trunk/debian/changelog 2014-01-08 17:24:38 UTC (rev 15731) +++ trunk/packages/anfo/trunk/debian/changelog 2014-01-08 18:33:08 UTC (rev 15732) @@ -1,11 +1,5 @@ -anfo (0.98-2biolinux1) precise; urgency=low +anfo (0.98-3) UNRELEASED; urgency=medium - * Build for Bio-Linux 7 - - -- Tim Booth <[email protected]> Wed, 08 Jan 2014 16:46:40 +0000 - -anfo (0.98-2) UNRELEASED; urgency=medium - [ Andreas Tille ] * fixed watch file * debian/control: @@ -16,12 +10,21 @@ * debian/copyright: DEP5 * use autoreconf (including necessary patches) * Create additional library packages + * debian/anfo.1: Check out manpage from upstream git + repository + * debian/upstream: Add link to upstream repository [ Gert Wollny ] * debian/patches/*: Patches to build with latest gcc - -- Andreas Tille <[email protected]> Wed, 01 Jan 2014 17:55:33 +0100 + -- Andreas Tille <[email protected]> Wed, 08 Jan 2014 19:23:24 +0100 +anfo (0.98-2biolinux1) precise; urgency=low + + * Build for Bio-Linux 7 + + -- Tim Booth <[email protected]> Wed, 08 Jan 2014 16:46:40 +0000 + anfo (0.98-1ubuntu4) lucid; urgency=low * Add zlib, bzlib, pkg-config, protobuf-compiler build deps. Modified: trunk/packages/anfo/trunk/debian/rules =================================================================== --- trunk/packages/anfo/trunk/debian/rules 2014-01-08 17:24:38 UTC (rev 15731) +++ trunk/packages/anfo/trunk/debian/rules 2014-01-08 18:33:08 UTC (rev 15732) @@ -18,6 +18,11 @@ debian/tmp/usr/lib/*/libanfo.so dh_install +override_dh_installman: + dh_installman + # delete unused manpage + find debian/anfo -name anfo-sge.1 -delete + # ./scm files should not be executable override_dh_fixperms : dh_fixperms Added: trunk/packages/anfo/trunk/debian/upstream =================================================================== --- trunk/packages/anfo/trunk/debian/upstream (rev 0) +++ trunk/packages/anfo/trunk/debian/upstream 2014-01-08 18:33:08 UTC (rev 15732) @@ -0,0 +1 @@ +Repository-Browse: https://github.com/udo-stenzel/anfo _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
