debian/0000755000000000000000000000000012257553775007210 5ustar debian/upstream0000644000000000000000000000150712257536226010766 0ustar Name: rtax Homepage: http://dev.davidsoergel.com/trac/rtax/ Bug-Database: http://dev.davidsoergel.com/trac/rtax/report/1 Bug-Submit: http://dev.davidsoergel.com/trac/rtax/newticket Changelog: http://hg.davidsoergel.com/rtax/src/tip/changelog Contact: dev@davidsoergel.com Repository: http://hg.davidsoergel.com/rtax Repository-Browse: http://hg.davidsoergel.com/rtax/src Reference: Author: David A W Soergel and Neelendu Dey and Rob Knight and Steven E Brenner Title: Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences Journal: The ISME Journal Year: 2012 Volume: 6 Pages: 1440–1444 DOI: 10.1038/ismej.2011.208 PMID: 22237546 URL: http://www.nature.com/ismej/journal/v6/n7/abs/ismej2011208a.html eprint: http://www.nature.com/ismej/journal/v6/n7/pdf/ismej2011208a.pdf debian/changelog0000644000000000000000000000107512257537424011056 0ustar rtax (0.984-2) unstable; urgency=medium * Team upload. * Corrected the name of the copyright holders. -- Charles Plessy Sat, 28 Dec 2013 12:56:34 +0100 rtax (0.984-1) unstable; urgency=low * Initial release. (Closes: #724280) * Removed broken magic to find scripts-subdir, because we know where rtax is installed (set_script_dir.path) * Change interpreter to bash to prevent syntax error warnings (fix-bash-syntax-error.patch) * Added minimal manpage. -- Simon Kainz Wed, 27 Nov 2013 09:50:23 +0100 debian/rtax.manpages0000644000000000000000000000001612257536226011670 0ustar debian/rtax.1 debian/compat0000644000000000000000000000000212257536226010376 0ustar 9 debian/rtax.install0000644000000000000000000000012412257536226011543 0ustar greengenes/* /usr/lib/rtax/greengenes scripts/* /usr/lib/rtax/scripts rtax /usr/bin debian/control0000644000000000000000000000146212257536226010606 0ustar Source: rtax Maintainer: Med Packaging Team Uploaders: Simon Kainz Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/rtax.git Vcs-Git: git://anonscm.debian.org/debian-med/rtax.git Homepage: http://dev.davidsoergel.com/rtax Package: rtax Architecture: all Depends: ${misc:Depends}, ${perl:Depends} Description: Classification of sequence reads of 16S ribosomal RNA gene Short-read technologies for microbial community profiling are increasingly popular, yet previous techniques for assigning taxonomy to paired-end reads perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads using a consensus algorithm. debian/source/0000755000000000000000000000000012257536226010500 5ustar debian/source/format0000644000000000000000000000001512257536226011707 0ustar 3.0 (quilt) debian/rules0000755000000000000000000000003712257536226010260 0ustar #!/usr/bin/make -f %: dh $@ debian/copyright0000644000000000000000000000365312257553503011137 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: RTAX Upstream-Contact: David A. W. Soergel Source: http://hg.davidsoergel.com/rtax Files: * Copyright: © 2011 Regents of the University of California License: BSD-3-clause License: BSD-3-clause 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 the University of California, Berkeley nor the names of its 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: © 2013 Simon Kainz , Andreas Tille License: BSD-3-clause debian/watch0000644000000000000000000000017012257536226010227 0ustar version=3 opts=uversionmangle=s/%20release// \ https://bitbucket.org/davidsoergel/rtax/downloads .*/(\d\S*)\.tar\.gz debian/rtax.10000644000000000000000000000365712257536226010253 0ustar .TH "rtax" 1 "27 Nov 2013" .SH "NAME" rtax - Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene .SH "SYNOPSIS" .B rtax [\fIOPTION\fR]... .SH DESCRIPTION .PP .SH OPTIONS .TP 13 .I \-r refd reference database in FASTA format .TP 13 .I \-t taxonomy taxonomy file with sequence IDs matching the reference database .TP 13 .I \-a queryA FASTA file containing query sequences (single-ended or read 1) .TP 13 .I \-b queryB FASTA file containing query sequences (read b, with matching IDs) .TP 13 .I \-x Reverse-complement query A sequences (required if they are provided in the reverse sense) .TP 13 .I \-y Reverse-complement query B sequences (required if they are provided in the reverse sense) .TP 13 .I \-i regex regular expression used to select part of the fasta header to use as the sequence id. Default: "(\\S+)" .TP 13 .I \-l file text file containing sequence IDs to process, one per line .TP 13 .I \-d delimiter delimiter separating the two reads when provided in a single file .TP 13 .I \-m tempdir temporary directory. Will be removed on successful completion, but likely not if there is an error. .TP 13 .I \-f for sequences where only one read is available, fall back to single-ended classification. Default: drop these sequences. .TP 13 .I \-g for sequences where one read is overly generic, do not fall back to single-ended classification. Default: classify these sequences based on only the more specific read. .TP 13 .I \-o classifications.out output path .SH EXAMPLES A quickstart example can be found here: \fIhttp://dev.davidsoergel.com/trac/rtax/wiki/QuickStart\fR .P Rtax can also be used within \fIQIIME\fR workflows, se this link for more information: \fIhttp://www.qiime.org/tutorials/rtax.html\fR .SH AUTHOR This manual page was written by Simon Kainz for the rtax package. .P Rtax was written by David A. W. Soergel . debian/patches/0000755000000000000000000000000012257536226010627 5ustar debian/patches/find_script_path.patch0000644000000000000000000000154012257536226015170 0ustar Author: Simon Kainz Last-Update: Tue, 27 Nov 2013 09:50:23 +0100 Description: Since in Debian the script dir is known this is pre-set here --- rtax-0.984.orig/rtax +++ rtax-0.984/rtax @@ -73,15 +73,7 @@ echoerr '' -# we want to call subsidiary scripts in the "scripts" subdir, but we don't know where we're installed or what the working directory is. -# solution from http://hintsforums.macworld.com/archive/index.php/t-73839.html - -IFS=$' \t\n' -#declare -x PATH=/bin:/usr/bin:/usr/local/bin -arg=$0; [[ -L $0 ]] && arg=$(stat -f '%Y' "$0") -pth=$(2>/dev/null cd "${arg%/*}" >&2; echo "`pwd -P`/${arg##*/}") -par=$(dirname "$pth") -scripts="$par/scripts" +scripts="/usr/lib/rtax/scripts" # The above solution works with the widespread GNU Coreutils 5.97. Thanks to Bernd Brandt for this alternate solution for Coreutils 8.5. debian/patches/series0000644000000000000000000000006312257536226012043 0ustar fix-bash-syntax-error.patch find_script_path.patch debian/patches/fix-bash-syntax-error.patch0000644000000000000000000000052412257536226016025 0ustar Author: Simon Kainz Last-Update: 2013-09-12 Description: Change script interpreter to /bin/bash Fixes syntax errors due to differnet if syntax between sh and bash. --- rtax-0.984.orig/greengenes/prepare-greengenes +++ rtax-0.984/greengenes/prepare-greengenes @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash cur=`pwd` debian/rtax.docs0000644000000000000000000000000712257536226011025 0ustar README