debian/0000775000000000000000000000000012253224404007166 5ustar debian/rules0000775000000000000000000000216412211763060010251 0ustar #!/usr/bin/make -f # Sample debian/rules for mothur # Andreas Tille # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 ARCHBITS ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS) %: dh $@ override_dh_auto_build: if [ $(ARCHBITS) -eq 64 ] ; then \ dh_auto_build -- 64BIT_VERSION=yes USEMPI=yes && \ mv mothur mothur-mpi && make clean && \ dh_auto_build -- 64BIT_VERSION=yes USEMPI=no ; \ else \ dh_auto_build -- 64BIT_VERSION=no ; \ fi override_dh_auto_install: true #Cleaning needs help right now override_dh_auto_clean: rm -f mothur mothur-mpi *.o mothur.*.logfile make clean ( cd uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr ) # Remark: The following uscan command requires devscripts > 2.12.4 which is not # yet released at the time of this package release. The code can be obtained # via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then use scripts/uscan.pl # Alternatively you can use # . debian/get-orig-source get-orig-source: uscan --verbose --force-download --repack-compression xz debian/watch0000664000000000000000000000022012211763060010211 0ustar version=3 opts=dversionmangle=s/(\+dfsg|[~\+]repack)// \ http://www.mothur.org/wiki/Download_mothur \ /w/images/.*/.*/Mothur\.([\d\.]+)\.zip debian/changelog0000664000000000000000000001367012253224400011043 0ustar mothur (1.31.2+dfsg-2build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Sat, 14 Dec 2013 22:58:48 -0500 mothur (1.31.2+dfsg-2) unstable; urgency=low * Team upload. * debian/patches/makefile.patch: Leave off -m64, which ia64 doesn't support and other 64-bit architectures don't need. (Closes: #721770.) -- Aaron M. Ucko Wed, 04 Sep 2013 22:37:31 -0400 mothur (1.31.2+dfsg-1) unstable; urgency=low * New upstream version * debian/watch: use dversionmangle to properly detect new upstream versions * debian/copyright: Add Files-Excluded to document what was removed from original source * debian/rules: Use enhanced uscan * debian/control: - cme fix dpkg-control - debhelper 9 - use anonscm for Vcs fields * debian/patches/uchime_hardening.patch: Hardening for uchime * debian/uchime.1 * debian/patches/spelling.patch: Some spelling corrections -- Andreas Tille Tue, 30 Jul 2013 14:32:44 +0200 mothur (1.27.0+repack-precise1) precise; urgency=low * Remove -march=native from makefile as this makes the result depend on the build machine - so a package built on a Core3 CPU won't work on a Xeon. -- Tim Booth Fri, 12 Oct 2012 11:41:04 +0100 mothur (1.27.0+repack-precise2) precise; urgency=low * New minor release from upstream * Build MPI version alongside regular version * ...but only for 64-bit -- Tim Booth Wed, 10 Oct 2012 11:20:43 +0100 mothur (1.25.0~repack-lucid3) lucid; urgency=low * Removed dependency on catchall - this belongs in the bio-linux-mothur package. Not sure what I was thinking there. -- Tim Booth Mon, 14 May 2012 10:57:22 +0100 mothur (1.25.0~repack-lucid2) lucid; urgency=low * Fix 32-bit build and add uchime (which should be packaged separately, but I've no time for that just now) -- Tim Booth Thu, 10 May 2012 10:43:04 +0100 mothur (1.25.0~repack-lucid1) lucid; urgency=low * Rebuild for Lucid with repack fudge again -- Tim Booth Wed, 09 May 2012 11:20:15 +0100 mothur (1.25.0-1) UNRELEASED; urgency=low * New upstream release * debian/upstream: more complete authors information in proper BibTeX format -- Andreas Tille Tue, 08 May 2012 18:00:19 +0200 mothur (1.24.1-1) unstable; urgency=low * New upstream version - adpated patches - droped debian/patches/kfreebsd.patch because it was applied upstream -- Andreas Tille Tue, 03 Apr 2012 09:05:44 +0200 mothur (1.23.1-1) unstable; urgency=low * New upstream version (including updating patches) * debian/upstream: - fixed typo: s/TITILE/TITLE/ - Moved DOI+PMID to references * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Build-Depends: gfortran * debian/get-orig-source: - be not that verbose - more reproducible creation of tarball - Strip some useless files from tarball (.*; *.o) * debhelper 9 (control+compat) * debian/copyright: DEP5 changes and verified using cme fix dpkg-copyright -- Andreas Tille Thu, 08 Mar 2012 14:52:47 +0100 mothur (1.22.2-2) unstable; urgency=low * debian/patches/kfreebsd.patch: Enable build on BSD machines (thanks to Christoph Egger and Robert Millan ) Closes: #650683 * debian/control: Fixed Vcs fields * debian/{control,rules}: drop explicite quilt dependency which is just given by source format 3.0 (quilt) -- Andreas Tille Tue, 06 Dec 2011 17:14:49 +0100 mothur (1.22.2~repack-ubuntu1) lucid; urgency=low * Backport for Ubuntu * Need to fudge version as upstream was repacked by Andreas' script -- Tim Booth Mon, 05 Dec 2011 17:37:16 +0000 mothur (1.22.2-1) unstable; urgency=low * New upstream version * debian/patches/drop_sse_option.patch: Fix for FTBFS: unrecognized command line option '-msse2' (Thanks for the patch to Nobuhiro Iwamatsu ) Closes: #648255 -- Andreas Tille Thu, 10 Nov 2011 08:38:32 +0100 mothur (1.22.1-1) unstable; urgency=low [ Thorsten Alteholz ] * new upstream version * adapted patches to this version * debian/control: no dependency on quilt needed * debian/control + debian/compat: dh version set to >= 8 [ Andreas Tille ] * debian/control: readd quilt dependency because build fails otherwise * debian/copyright: fix spelling error -- Andreas Tille Mon, 07 Nov 2011 11:14:17 +0100 mothur (1.18.1-1) unstable; urgency=low * New upstream version (adapted patches to new location of makefile) * debian/rules: No need to specify SOURCEDIR any more * Added Tim Booth as Uploader, removed Sri Girish Srinivasa Murthy from uploaders * Standards-Version: 3.9.2 (no changes needed) -- Andreas Tille Tue, 26 Apr 2011 19:58:45 +0200 mothur (1.18.0-1ubuntu1) lucid; urgency=low * Rebuild for PPA * Source now comes in subdirectory Mothur.source - modify rules file to handle this -- Tim Booth Thu, 14 Apr 2011 14:50:24 +0100 mothur (1.17.3-1) unstable; urgency=low * New upstream version, which specifically solves some copyright questions of ftpmaster (Charles, thanks for reviewing debian/copyright) Closes: #589675 * Updated patches * debian/copyright: Clarified license issues -- Andreas Tille Wed, 30 Mar 2011 09:01:52 +0200 mothur (1.15.0-1ubuntu1) lucid; urgency=low * Rebuild for upload to PPA, license or not. -- Tim Booth Sun, 30 Jan 2011 12:14:18 +0000 mothur (1.15.0-1) unstable; urgency=low * Initial release (Closes: #589675) -- Andreas Tille Wed, 02 Feb 2011 08:59:45 +0100 debian/get-orig-source0000664000000000000000000000137612211763060012133 0ustar #!/bin/sh # script to download and repack source package of mothur because it is provided as zip # set -x PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` VERSION=`uscan --verbose --force-download | \ grep "Newest version on remote site is .* local version is .*" | \ head -n 1 | \ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"` UPSTREAMNAME=Mothur mkdir -p ../tarballs cd ../tarballs UPSTREAMDIR="${PKG}-${VERSION}" unzip -q ../${UPSTREAMNAME}.${VERSION}.zip mv Mothur.source ${UPSTREAMDIR} find ${UPSTREAMDIR} -name ".*" | xargs rm -f find ${UPSTREAMDIR} -name "*.o" | xargs rm -f XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -caf "$PKG"_"$VERSION".orig.tar.xz "${UPSTREAMDIR}" rm -rf "${UPSTREAMDIR}" __MACOSX debian/upstream0000664000000000000000000000137312211763060010755 0ustar Contact: Patrick D. Schloss Homepage: http://www.mothur.org Name: Mothur Reference: AUTHOR: Patrick D Schloss and Sarah L Westcott and Thomas Ryabin and Justine R Hall and Martin Hartmann and Emily B Hollister and Ryan A Lesniewski and Brian B Oakley and Donovan H Parks and Courtney J Robinson and Jason W Sahl and Blaz Stres and Gerhard G Thallinger and David J Van Horn and Carolyn F Weber TITLE: > Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities JOURNAL: Appl Environ Microbiol YEAR: 2009 PAGES: 7537-7541 VOLUME: 75 NUMBER: 23 URL: http://aem.asm.org/cgi/content/full/75/23/7537 ISSN: 1098-5336 DOI: 10.1128/AEM.01541-09 PMID: 19801464 debian/compat0000664000000000000000000000000212211763060010364 0ustar 9 debian/mothur.install0000664000000000000000000000004012211763060012066 0ustar mothur /usr/bin uchime /usr/bin debian/uchime.10000664000000000000000000002634612211763060010535 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH UCHIME "1" "July 2013" "uchime v4.2.40" "User Commands" .SH NAME uchime \- reads a fasta file and reference file and outputs potentially chimeric sequences .SH DESCRIPTION The chimera.uchime command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar. .SH SYNOPSIS .B uchime \fB\-\-input\fR query.fasta [\-\-db db.fasta] [\-\-uchimeout results.uchime] .IP [\-\-uchimealns results.alns] .SH OPTIONS .PP \fB\-\-input\fR filename .IP Query sequences in FASTA format. If the \fB\-\-db\fR option is not specificed, uchime uses de novo detection. In de novo mode, relative abundance must be given by a string /ab=xxx/ somewhere in the label, where xxx is a floating\-point number, e.g. >F00QGH67HG/ab=1.2/. .PP \fB\-\-db\fR filename .IP Reference database in FASTA format. Optional, if not specified uchime uses de novo mode. .IP ***WARNING*** The database is searched ONLY on the plus strand. You MUST include reverse\-complemented sequences in the database if you want both strands to be searched. .PP \fB\-\-abskew\fR x .IP Minimum abundance skew. Default 1.9. De novo mode only. Abundance skew is: .IP min [ abund(parent1), abund(parent2) ] / abund(query). .PP \fB\-\-uchimeout\fR filename .IP Output in tabbed format with one record per query sequence. First field is score (h), second field is query label. For details, see manual. .PP \fB\-\-uchimealns\fR filename .IP Multiple alignments of query sequences to parents in humanreadable format. Alignments show columns with differences that support or contradict a chimeric model. .PP \fB\-\-minh\fR h .IP Mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease \fB\-\-xn\fR, you may need to increase \fB\-\-minh\fR, and vice versa. .PP \fB\-\-mindiv\fR div .IP Minimum divergence ratio, default 0.5. Div ratio is 100% \- %identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase \fB\-\-mindiv\fR to, say, 1.0 or 2.0, and also decrease \fB\-\-min\fR h, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark. .PP \fB\-\-xn\fR beta .IP Weight of a no vote, also called the beta parameter. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data. .PP \fB\-\-dn\fR n .IP Pseudo\-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2. .PP \fB\-\-xa\fR w .IP Weight of an abstain vote. Default 1. So far, results do not seem to be very sensitive to this parameter, but if you have a good training set might be worth trying. Reasonable values might range from 0.1 to 2. .PP \fB\-\-chunks\fR n .IP Number of chunks to extract from the query sequence when searching for parents. Default 4. .PP \fB\-\-[no]ovchunks\fR .IP [Do not] use overlapping chunks. Default do not. .PP \fB\-\-minchunk\fR n .IP Minimum length of a chunk. Default 64. .PP \fB\-\-idsmoothwindow\fR w .IP Length of id smoothing window. Default 32. .PP \fB\-\-minsmoothid\fR f .IP Minimum factional identity over smoothed window of candidate parent. Default 0.95. .PP \fB\-\-maxp\fR n .IP Maximum number of candidate parents to consider. Default 2. In tests so far, increasing \fB\-\-maxp\fR gives only a very small improvement in sensivity but tends to increase the error rate quite a bit. .PP \fB\-\-[no]skipgaps\fR \fB\-\-[no]skipgaps2\fR .IP These options control how gapped columns affect counting of diffs. If \fB\-\-skipgaps\fR is specified, columns containing gaps do not found as diffs. If \fB\-\-skipgaps2\fR is specified, if column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default is \fB\-\-skipgaps\fR \fB\-\-skipgaps2\fR. .PP \fB\-\-minlen\fR L \fB\-\-maxlen\fR L .IP Minimum and maximum sequence length. Defaults 10, 10000. Applies to both query and reference sequences. .PP \fB\-\-ucl\fR .IP Use local\-X alignments. Default is global\-X. On tests so far, global\-X is always better; this option is retained because it just might work well on some future type of data. .PP \fB\-\-queryfract\fR f .IP Minimum fraction of the query sequence that must be covered by a local\-X alignment. Default 0.5. Applies only when \fB\-\-ucl\fR is specified. .PP \fB\-\-quiet\fR .IP Do not display progress messages on stderr. .PP \fB\-\-log\fR filename .IP Write miscellaneous information to the log file. Mostly of interest to me (the algorithm developer). Use \fB\-\-verbose\fR to get more info. .PP \fB\-\-self\fR .IP In reference database mode, exclude a reference sequence if it has the same label as the query. This is useful for benchmarking by using the ref db as a query to test for false positives. .TP \fB\-\-abskew\fR help .TP \fB\-\-absort\fR help .TP \fB\-\-abx\fR help .TP \fB\-\-allpairs\fR help .TP \fB\-\-alpha\fR help .TP \fB\-\-band\fR help .TP \fB\-\-blast6out\fR help .TP \fB\-\-[no]blast_termgaps\fR help .TP \fB\-\-blastout\fR help .TP \fB\-\-bump\fR help .TP \fB\-\-[no]cartoon_orfs\fR help .TP \fB\-\-cc\fR help .TP \fB\-\-chain_evalue\fR help .TP \fB\-\-chain_targetfract\fR help .TP \fB\-\-chainhits\fR help .TP \fB\-\-chainout\fR help .TP \fB\-\-chunks\fR help .TP \fB\-\-clstr2uc\fR help .TP \fB\-\-clump\fR help .TP \fB\-\-clump2fasta\fR help .TP \fB\-\-clumpfasta\fR help .TP \fB\-\-clumpout\fR help .TP \fB\-\-cluster\fR help .TP \fB\-\-compilerinfo\fR Write info about compiler types and #defines to stdout. .TP \fB\-\-computekl\fR help .TP \fB\-\-db\fR help .TP \fB\-\-dbstep\fR help .TP \fB\-\-[no]denovo\fR help .TP \fB\-\-derep\fR help .TP \fB\-\-diffchar\fR help .TP \fB\-\-dn\fR help .TP \fB\-\-doug\fR help .TP \fB\-\-droppct\fR help .TP \fB\-\-evalue\fR help .TP \fB\-\-evalue_g\fR help .TP \fB\-\-exact\fR help .TP \fB\-\-[no]fastalign\fR help .TP \fB\-\-fastapairs\fR help .TP \fB\-\-fastq2fasta\fR help .TP \fB\-\-findorfs\fR help .TP \fB\-\-[no]flushuc\fR help .TP \fB\-\-frame\fR help .TP \fB\-\-fspenalty\fR help .TP \fB\-\-gapext\fR help .TP \fB\-\-gapopen\fR help .TP \fB\-\-getseqs\fR help .TP \fB\-\-global\fR help .TP \fB\-\-hash\fR help .TP \fB\-\-hashsize\fR help .TP \fB\-\-help\fR Display command\-line options. .TP \fB\-\-hireout\fR help .TP \fB\-\-hspalpha\fR help .TP \fB\-\-id\fR help .TP \fB\-\-idchar\fR help .TP \fB\-\-iddef\fR help .TP \fB\-\-idprefix\fR help .TP \fB\-\-ids\fR help .TP \fB\-\-idsmoothwindow\fR help .TP \fB\-\-idsuffix\fR help .TP \fB\-\-indexstats\fR help .TP \fB\-\-input\fR help .TP \fB\-\-[no]isort\fR help .TP \fB\-\-k\fR help .TP \fB\-\-ka_dbsize\fR help .TP \fB\-\-ka_gapped_k\fR help .TP \fB\-\-ka_gapped_lambda\fR help .TP \fB\-\-ka_ungapped_k\fR help .TP \fB\-\-ka_ungapped_lambda\fR help .TP \fB\-\-[no]label_ab\fR help .TP \fB\-\-labels\fR help .TP \fB\-\-[no]leftjust\fR help .TP \fB\-\-lext\fR help .TP \fB\-\-local\fR help .TP \fB\-\-log\fR Log file name. .TP \fB\-\-[no]log_hothits\fR help .TP \fB\-\-[no]log_query\fR help .TP \fB\-\-[no]logmemgrows\fR help .TP \fB\-\-logopts\fR Log options. .TP \fB\-\-[no]logwordstats\fR help .TP \fB\-\-lopen\fR help .TP \fB\-\-makeindex\fR help .TP \fB\-\-match\fR help .TP \fB\-\-matrix\fR help .TP \fB\-\-max2\fR help .TP \fB\-\-maxaccepts\fR help .TP \fB\-\-maxclump\fR help .TP \fB\-\-maxlen\fR help .TP \fB\-\-maxovd\fR help .TP \fB\-\-maxp\fR help .TP \fB\-\-maxpoly\fR help .TP \fB\-\-maxqgap\fR help .TP \fB\-\-maxrejects\fR help .TP \fB\-\-maxspan1\fR help .TP \fB\-\-maxspan2\fR help .TP \fB\-\-maxtargets\fR help .TP \fB\-\-maxtgap\fR help .TP \fB\-\-mcc\fR help .TP \fB\-\-mergeclumps\fR help .TP \fB\-\-mergesort\fR help .TP \fB\-\-minchunk\fR help .TP \fB\-\-mincodons\fR help .TP \fB\-\-mindiffs\fR help .TP \fB\-\-mindiv\fR help .TP \fB\-\-minh\fR help .TP \fB\-\-minhsp\fR help .TP \fB\-\-minlen\fR help .TP \fB\-\-minorfcov\fR help .TP \fB\-\-minspanratio1\fR help .TP \fB\-\-minspanratio2\fR help .TP \fB\-\-[no]minus_frames\fR help .TP \fB\-\-mismatch\fR help .TP \fB\-\-mkctest\fR help .TP \fB\-\-[no]nb\fR help .TP \fB\-\-optimal\fR help .TP \fB\-\-orfstyle\fR help .TP \fB\-\-otusort\fR help .TP \fB\-\-output\fR help .TP \fB\-\-[no]output_rejects\fR help .TP \fB\-\-probmx\fR help .TP \fB\-\-query\fR help .TP \fB\-\-queryfract\fR help .TP \fB\-\-querylen\fR help .TP \fB\-\-quiet\fR Turn off progress messages. .TP \fB\-\-randseed\fR help .TP \fB\-\-realign\fR help .TP \fB\-\-[no]rev\fR help .TP \fB\-\-[no]rightjust\fR help .TP \fB\-\-rowlen\fR help .TP \fB\-\-secs\fR help .TP \fB\-\-seeds\fR help .TP \fB\-\-seedsout\fR help .TP \fB\-\-seedt1\fR help .TP \fB\-\-seedt2\fR help .TP \fB\-\-self\fR help .TP \fB\-\-[no]selfid\fR help .TP \fB\-\-simcl\fR help .TP \fB\-\-[no]skipgaps\fR help .TP \fB\-\-[no]skipgaps2\fR help .TP \fB\-\-sort\fR help .TP \fB\-\-sortuc\fR help .TP \fB\-\-sparsedist\fR help .TP \fB\-\-sparsedistparams\fR help .TP \fB\-\-split\fR help .TP \fB\-\-[no]ssort\fR help .TP \fB\-\-sspenalty\fR help .TP \fB\-\-[no]stable_sort\fR help .TP \fB\-\-staralign\fR help .TP \fB\-\-stepwords\fR help .TP \fB\-\-strand\fR help .TP \fB\-\-targetfract\fR help .TP \fB\-\-targetlen\fR help .TP \fB\-\-tmpdir\fR help .TP \fB\-\-[no]trace\fR help .TP \fB\-\-tracestate\fR help .TP \fB\-\-[no]trunclabels\fR help .TP \fB\-\-[no]twohit\fR help .TP \fB\-\-uc\fR help .TP \fB\-\-uc2clstr\fR help .TP \fB\-\-uc2fasta\fR help .TP \fB\-\-uc2fastax\fR help .TP \fB\-\-uchime\fR help .TP \fB\-\-uchimealns\fR help .TP \fB\-\-uchimeout\fR help .TP \fB\-\-[no]ucl\fR help .TP \fB\-\-uhire\fR help .TP \fB\-\-ungapped\fR help .TP \fB\-\-userfields\fR help .TP \fB\-\-userout\fR help .TP \fB\-\-usersort\fR help .TP \fB\-\-uslink\fR help .TP \fB\-\-[no]usort\fR help .TP \fB\-\-utax\fR help .TP \fB\-\-[no]verbose\fR help .TP \fB\-\-version\fR Show version and exit. .TP \fB\-\-w\fR help .TP \fB\-\-weak_evalue\fR help .TP \fB\-\-weak_id\fR help .TP \fB\-\-[no]wordcountreject\fR help .TP \fB\-\-[no]wordweight\fR help .TP \fB\-\-xa\fR help .TP \fB\-\-xdrop_g\fR help .TP \fB\-\-xdrop_nw\fR help .TP \fB\-\-xdrop_u\fR help .TP \fB\-\-xdrop_ug\fR help .TP \fB\-\-xframe\fR help .TP \fB\-\-xlat\fR help .TP \fB\-\-xn\fR help .SH AUTHOR Robert C. Edgar .SH SEE ALSO http://www.drive5.com/uchime debian/copyright0000664000000000000000000001105612211763060011124 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Mothur Upstream-Contact: Patrick D. Schloss Source: http://www.mothur.org/wiki/Download_mothur Files-Excluded: .* */.* */*.o __MACOSX/ mothur uchime_src/mk.std[eo]* uchime_src.zip Files: * Copyright: © 2009-2012 Schloss Lab UMASS Amhers., Patrick Schloss License: GPL-3 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. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . Comment: On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. . The license is statet in the file mothur.cpp and at the project web page http://www.mothur.org/wiki/Mothur_license Please note that not every single file in the source is edited to reflect the license, however we got confirmation about this license from upstream. Files: clearcut.* cmdargs.* common.h dayhoff.h distclearcut.* dmat.* fasta.* prng.* Copyright: © 2004, Luke Sheneman © 1997 - 2002, Makoto Matsumoto and Takuji Nishimura License: Clearcut 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. + The names of its contributors may not 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: getopt_long.* Copyright: © 2004 Koji Arai License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Comment: This getopt_long() is compatible with GNU's, however, added original extension (short 1 byte option). Files: debian/* Copyright: © 2010 Sri Girish Srinivasa Murthy © 2011-2012 Andreas Tille License: GPL-3 On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. debian/mothur.10000664000000000000000000000152112211763060010565 0ustar .TH MOTHUR 1 "2011-01-30" .SH NAME mothur \- sequence analysis suite for research on microbiota .SH SYNOPSIS .B mothur [ batchfile ] .SH DESCRIPTION This manual page documents briefly the .B mothur command. .PP \fBMothur\fP seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It has incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, a number of other features including calculators and visualization tools were added. .SH SEE ALSO Online manual .BR http://www.mothur.org/wiki/Mothur_manual .SH AUTHOR #PACKAGE# was written by . .PP This manual page was written by #USERNAME# <#EMAIL#>, for the Debian project (and may be used by others). debian/source/0000775000000000000000000000000012211767450010475 5ustar debian/source/format0000664000000000000000000000001412211763060011674 0ustar 3.0 (quilt) debian/manpages0000664000000000000000000000001312211763060010676 0ustar debian/*.1 debian/README.Debian0000664000000000000000000000040312211763060011224 0ustar mothur for Debian ----------------- If you start mothur you can get help by issuing help(). You also might like to read the online manual at http://www.mothur.org/wiki/Mothur_manual -- Andreas Tille Sun, 30 Jan 2011 00:21:42 +0100 debian/mothur-mpi.install0000664000000000000000000000002412211763060012653 0ustar mothur-mpi /usr/bin debian/install0000664000000000000000000000006312211763060010556 0ustar mothur /usr/bin mothurMPI /usr/bin uchime /usr/bin debian/menu0000664000000000000000000000026012211763060010053 0ustar ?package(mothur):needs="text" section="Applications/Science/Biology"\ title="Mothur" command="/usr/bin/mothur" \ hints="sequence analysis suite for research on microbiota" debian/README.Source0000664000000000000000000000104712211763060011307 0ustar Hints for mothur on cluster machines: ------------------------------------- If you would like to build a mpi-enabled version of mothur, you will want to change the no to yes below. If you are running mothur on a single machine and not a cluster, the mpi-enabled version is slower than using the non-mpi enabled version. USEMPI ?= no ifeq ($(strip $(USEMPI)),yes) CXX = mpic++ CXXFLAGS += -DUSE_MPI endif (see http://www.mothur.org/wiki/Makefile_options#MPI_Version) -- Andreas Tille Sun, 30 Jan 2011 00:21:42 +0100 debian/control0000664000000000000000000000273712211763060010602 0ustar Source: mothur Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Tim Booth Section: science Priority: optional Build-Depends: debhelper (>= 9), libreadline-dev, gfortran, libopenmpi-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mothur/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mothur/trunk/ Homepage: http://www.mothur.org Package: mothur Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Conflicts: uchime Provides: uchime Description: sequence analysis suite for research on microbiota Mothur seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It has incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, a number of other features including calculators and visualization tools were added. Package: mothur-mpi Architecture: amd64 Depends: ${shlibs:Depends}, ${misc:Depends}, mothur, openmpi-bin Description: mpi-enabled binary for mothur Provides the MPI-enabled binary for Mothur According to the docs this is of limited usefulness but is provided for completeness. debian/mothur-mpi.links0000664000000000000000000000010212211763060012322 0ustar usr/share/man/man1/mothur.1.gz usr/share/man/man1/mothur-mpi.1.gz debian/patches/0000775000000000000000000000000012211767450010624 5ustar debian/patches/catchall_fix.patch0000664000000000000000000000177112211763060014265 0ustar This removes a workaround that is better fixed in Catchall than in Mothur, so I did that (packaged in bio-linux-catchall just now as I don't have the source compiling yet.) --- a/catchallcommand.cpp +++ b/catchallcommand.cpp @@ -198,6 +198,7 @@ int CatchAllCommand::execute() { if (abort == true) { if (calledHelp) { return 0; } return 2; } + /* TB for Bio-Linux: Don't need this... //get location of catchall path = m->argv; path = path.substr(0, (path.find_last_of("othur")-5)); @@ -246,6 +247,11 @@ int CatchAllCommand::execute() { //prepare full output directory outputDir = m->getFullPathName(outputDir); + */ + + /* TB for Bio-Linux: We just need this, assuming catchall is properly wrapped to avoid + * the bug described above - see the bio-linux-catchall package */ + string catchAllCommandExe = "catchall "; if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); } debian/patches/makefile.patch0000664000000000000000000000230712211763626013425 0ustar Author: Steffen Moeller , Tim Booth Purpose: Comment MAC specific option Don't bother with any compilation flags, as the defaults are already sane on all architectures (and trying to set -m64 explicitly fails on ia64). --- a/makefile +++ b/makefile @@ -21,14 +21,15 @@ FORTAN_COMPILER = gfortran FORTRAN_FLAGS = # Optimize to level 3: -CXXFLAGS += -O3 +# Nope, let debuild set this. +# CXXFLAGS += -O3 ifeq ($(strip $(64BIT_VERSION)),yes) #if you are using centos uncomment the following lines #CXX = g++44 #if you are a mac user use the following line - TARGET_ARCH += -arch x86_64 + #TARGET_ARCH += -arch x86_64 #if you using cygwin to build Windows the following line #CXX = x86_64-w64-mingw32-g++ @@ -38,9 +39,11 @@ ifeq ($(strip $(64BIT_VERSION)),yes) #if you are a linux user use the following line #CXXFLAGS += -mtune=native -march=native -m64 + # But not if you are trying to make a generic build for + # packaging, because your binary will end up being specific + # to your processor. CXXFLAGS += -DBIT_VERSION - FORTRAN_FLAGS = -m64 endif @@ -120,4 +123,3 @@ install : mothur clean : @rm -f $(OBJECTS) @rm -f uchime - debian/patches/series0000664000000000000000000000023712211763060012034 0ustar makefile.patch no_lcurses.patch drop_sse_option.patch catchall_fix.patch build_without_tty.patch uchime_link_dynamically uchime_hardening.patch spelling.patch debian/patches/no_lcurses.patch0000664000000000000000000000053312211763060014013 0ustar Author: Andreas Tille Date: 2011-01-30 Dscription: There is no need to link against lncurses because its symbols are not used --- a/makefile +++ b/makefile @@ -68,8 +68,7 @@ endif ifeq ($(strip $(USEREADLINE)),yes) CXXFLAGS += -DUSE_READLINE LIBS = \ - -lreadline\ - -lncurses + -lreadline endif debian/patches/build_without_tty.patch0000664000000000000000000000054412211763060015423 0ustar --- a/uchime_src/mk +++ b/uchime_src/mk @@ -6,7 +6,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr for CPPName in $CPPNames do - echo $CPPName >> /dev/tty + echo $CPPName >&2 g++ $ENV_GCC_OPTS -c -O2 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr cat tmp.stderr cat tmp.stderr >> mk.stderr debian/patches/uchime_link_dynamically0000664000000000000000000000074412211763060015422 0ustar Unfortunately there is no explanation for why the upstream does not build this dynamically. I'm therefore commenting it out until someone shouts. --- a/uchime_src/mk +++ b/uchime_src/mk @@ -14,9 +14,9 @@ do done LINK_OPTS= -if [ `uname -s` == Linux ] ; then - LINK_OPTS=-static -fi +#if [ `uname -s` == Linux ] ; then +# LINK_OPTS=-static +#fi g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr cat tmp.stderr cat tmp.stderr >> mk.stderr debian/patches/uchime_hardening.patch0000664000000000000000000000103412211763060015125 0ustar Author: Andreas Tille LastChanged: Tue, 30 Jul 2013 21:21:02 +0200 Description: Propagate hardening options to uchime --- a/makefile +++ b/makefile @@ -105,7 +105,9 @@ mothur : fortranSource $(OBJECTS) uchime strip mothur uchime: - cd uchime_src && ./mk && mv uchime .. && cd .. + echo ENV_GCC_OPTS="$(CPPFLAGS)" + echo ENV_LINK_OPTS="$(LDFLAGS)" + cd uchime_src && ENV_GCC_OPTS="$(CPPFLAGS)" ENV_LINK_OPTS="$(LDFLAGS)" ./mk && mv uchime .. && cd .. fortranSource: ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f debian/patches/drop_sse_option.patch0000664000000000000000000000126112211763060015044 0ustar Author: Nobuhiro Iwamatsu Date: Thu, 10 Nov 2011 00:39:01 UTC Closes: #648255 Description: Fix for FTBFS: cc1plus: error: unrecognized command line option '-msse2' --- a/uchime_src/mk +++ b/uchime_src/mk @@ -7,7 +7,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr for CPPName in $CPPNames do echo $CPPName >> /dev/tty - g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr + g++ $ENV_GCC_OPTS -c -O2 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr cat tmp.stderr cat tmp.stderr >> mk.stderr rm -f tmp.stderr debian/patches/spelling.patch0000664000000000000000000002313712211763060013461 0ustar Author: Andreas Tille LastChanged: Tue, 30 Jul 2013 21:21:02 +0200 Description: Some spelling corrections Note: There are similar spelling problems in comments inside the code that are not fixed by this patch --- a/getcurrentcommand.cpp +++ b/getcurrentcommand.cpp @@ -31,7 +31,7 @@ string GetCurrentCommand::getHelpString( string helpString = ""; helpString += "The get.current command outputs the current files saved by mothur.\n"; helpString += "The get.current command has one parameter: clear.\n"; - helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n"; + helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n"; helpString += "The get.current command should be in the following format: \n"; helpString += "get.current() or get.current(clear=fasta-name-accnos)\n"; return helpString; --- a/setcurrentcommand.cpp +++ b/setcurrentcommand.cpp @@ -56,7 +56,7 @@ string SetCurrentCommand::getHelpString( string helpString = ""; helpString += "The set.current command allows you to set the current files saved by mothur.\n"; helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary and taxonomy.\n"; - helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n"; + helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n"; helpString += "The set.current command should be in the following format: \n"; helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n"; return helpString; --- a/matrixoutputcommand.cpp +++ b/matrixoutputcommand.cpp @@ -773,7 +773,7 @@ int MatrixOutputCommand::driver(vector