debian/0000755000000000000000000000000012173165167007177 5ustar debian/control0000644000000000000000000001055412173164626010606 0ustar Source: microbiomeutil Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Tim Booth , Andreas Tille Build-Depends: debhelper (>= 9), cdbfasta, blast2 Standards-Version: 3.9.4 Homepage: http://microbiomeutil.sourceforge.net/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/microbiomeutil/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/microbiomeutil/trunk/ Package: microbiomeutil Architecture: all Depends: ${misc:Depends}, chimeraslayer, nast-ier, wigeon Description: Microbiome Analysis Utilities The microbiomeutil package comes with the following utilities: * ChimeraSlayer: ChimeraSlayer for chimera detection. * NAST-iEr: NAST-based alignment tool. * WigeoN: A reimplementation of the Pintail 16S anomaly detection utility * RESOURCES: Reference 16S sequences and NAST-alignments that the tools above leverage. Package: chimeraslayer Architecture: all Depends: ${misc:Depends}, microbiomeutil-data, cdbfasta, blast2 Recommends: nast-ier Description: detects likely chimeras in PCR amplified DNA ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500bp). . Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences: . 1. the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera 2. candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence 3. the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment to the selected reference parent sequences 4. an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences. . To run Chimera Slayer, you need NAST-formatted sequences generated by the nast-ier utility. . ChimeraSlayer is part of the microbiomeutil suite. Package: nast-ier Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, microbiomeutil-data, cdbfasta Description: NAST-based DNA alignment tool The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences. . The alignment algorithm involves global dynamic programming profile alignment to fixed (NAST-formatted) multiply aligned template sequences without any end-gap penalty. . NAST-iEr is part of the microbiomeutil suite. Package: wigeon Architecture: all Depends: ${misc:Depends}, microbiomeutil-data Recommends: nast-ier Description: reimplementation of the Pintail 16S DNA anomaly detection utility WigeoN examines the sequence conservation between a query and a trusted reference sequence, both in NAST alignment format. Based on the sequence identity between the query and the reference sequence, there is an expected amount of variation among the alignment. If the observed variation is greater than the 95% quantile of the distribution of variation observed between non-anomalous sequences, then it is flagged as an anomaly. . WigeoN is a flexible command-line based reimplementation of the Pintail algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36. . WigeoN is useful for flagging chimeras and anomalies only in near full-length 16S rRNA sequences. WigeoN lacks sensitivity with sequences less than 1000 bp. . To run WigeoN, you need NAST-formatted sequences generated by the nast-ier utility. . WigeoN is part of the microbiomeutil suite. Package: microbiomeutil-data Architecture: all Depends: ${misc:Depends} Enhances: chimeraslayer, nast-ier, wigeon Description: Reference 16S sequences and NAST-alignments used by microbiomeutil tools Reference data for tools in the microbiomeutil package. The algorithms used by the tools chimeraslayer, nast-ier and wigeon are based on reference data which are provided by this package. debian/microbiomeutil-data.install0000644000000000000000000000037412153326700014513 0ustar RESOURCES /usr/share/microbiomeutil-data ChimeraSlayer/sample_data/* /usr/share/microbiomeutil-data/ChimeraSlayer WigeoN/sample_data/* /usr/share/microbiomeutil-data/ChimeraSlayer NAST-iEr/sample_data/* /usr/share/microbiomeutil-data/ChimeraSlayer debian/nast-ier.10000644000000000000000000000233412153374663011006 0ustar .TH NAST-IER "1" "June 2013" "nast-ier " "User Commands" .SH NAME nast-ier \- NAST-based DNA alignment tool .SH DESCRIPTION The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences. .PP The alignment algorithm involves global dynamic programming profile alignment to fixed (NAST-formatted) multiply aligned template sequences without any end-gap penalty. .PP NAST-iEr is part of the microbiomeutil suite. .SH OPTIONS .SS Required: .IP \fB\-\-query_FASTA\fR query database in FASTA format (seqs to NAST\-align) .SS Optional: (unless defaults are not set!) .IP \fB\-\-db_NAST\fR reference database in NAST format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta\fP) .IP \fB\-\-db_FASTA\fR reference database in FASTA format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.fasta\fP) .IP \fB\-\-num_top_hits\fR number of top hits to use for profile\-alignment (default: 10) .IP \fB\-\-Evalue\fR Evalue cutoff for top hits (default: 1e\-50) .SH "SEE ALSO" http://microbiomeutil.sourceforge.net/#A_NASTiEr .SH AUTHOR This manual page was written by Andreas Tille but can be freely used for any other distribution. debian/chimeraslayer.10000644000000000000000000000650512153372710012107 0ustar .TH CHIMERASLAYER "1" "June 2013" "chimeraslayer " "User Commands" .SH NAME chimeraslayer \- detects likely chimeras in PCR amplified DNA .SH DESCRIPTION ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500bp). .PP Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences: .IP 1. the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera .IP 2. candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence .IP 3. the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment to the selected reference parent sequences .IP 4. an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences. .PP To run Chimera Slayer, you need NAST-formatted sequences generated by the nast-ier utility. .PP ChimeraSlayer is part of the microbiomeutil suite. .SH OPTIONS .SS Required .IP \fB\-\-query_NAST\fR multi\-fasta file containing query sequences in alignment format .PP .SS Common options .IP \fB\-\-db_NAST\fR db in NAST format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta\fP) .IP \fB\-\-db_FASTA\fR db in fasta format (megablast formatted) (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.fasta\fP) .IP \fB\-n\fR number of top matching database sequences to compare to (default 15) .IP \fB\-R\fR min divergence ratio default: 1.007 .IP \fB\-P\fR min percent identity among matching sequences (default: 90) .SS Parameters to tune ChimeraParentSelector: Scoring parameters: .IP \fB\-M\fR match score (default: +5) .IP \fB\-N\fR mismatch penalty (default: \fB\-4\fR) .IP \fB\-Q\fR min query coverage by matching database sequence (default: 70) .IP \fB\-T\fR maximum traverses of the multiple alignment (default: 1) .SS Parameters to tune ChimeraPhyloChecker .IP \fB\-\-windowSize\fR default 50 .IP \fB\-\-windowStep\fR default 5 .IP \fB\-\-minBS\fR minimum bootstrap support for calling chimera (default: 90) .IP \fB\-\-num_BS_replicates\fR default: 100 .IP \fB\-\-low_range_finer_BS\fR (default: 10) If computed BS is between minBS and (minBS \- low_range_finer_BS), then num_finer_BS_replicates computed. .IP \fB\-\-num_finer_BS_replicates\fR (default: 1000) .IP \fB\-S\fR percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) .IP \fB\-\-num_parents_test\fR number of potential parents to test for chimeras (default: 3) .IP \fB\-\-MAX_CHIMERA_PARENT_PER_ID\fR Chimera/Parent alignments with perID above this are considered non\-chimeras (default 100; turned off) .SS Misc options .IP \fB\-\-printFinalAlignments\fR shows alignment between query sequence and pair of candidate chimera parents .IP \fB\-\-printCSalignments\fR print ChimeraSlayer alignments in ChimeraSlayer output .IP \fB\-\-exec_dir\fR chdir to here before running .SH "SEE ALSO" http://microbiomeutil.sourceforge.net/#A_CS .SH AUTHOR This manual page was written by Andreas Tille but can be freely used for any other distribution. debian/microbiomeutil.links0000644000000000000000000000047212153400310013243 0ustar usr/bin/chimeraslayer usr/bin/ChimeraSlayer usr/bin/nast-ier usr/bin/NAST-iEr usr/bin/wigeon usr/bin/WigeoN usr/share/man/man1/chimeraslayer.1.gz usr/share/man/man1/ChimeraSlayer.1.gz usr/share/man/man1/nast-ier.1.gz usr/share/man/man1/NAST-iEr.1.gz usr/share/man/man1/wigeon.1.gz usr/share/man/man1/WigeoN.1.gz debian/chimeraslayer.links0000644000000000000000000000007512153326147013066 0ustar usr/lib/ChimeraSlayer/ChimeraSlayer.pl usr/bin/chimeraslayer debian/microbiomeutil.docs0000644000000000000000000000015511544546650013076 0ustar README docs # As a reminder for the separation of packages #NAST-iEr/README #RESOURCES/README #WigeoN/README debian/cm_to_wigeon.10000644000000000000000000000273612153402721011726 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.2. .TH CM_TO_WIGEON "1" "June 2013" "cm_to_wigeon " "User Commands" .SH NAME cm_to_wigeon \- helper for wigeon (Pintail 16S DNA anomaly detection) .SH DESCRIPTION \fBUnfortunately this tools that comes in connection with wigeon(1) is not documented but it regards the options below. If you know better about its purpose please drop us a note using reportbug on your Debian system.\fR .SH OPTIONS .SS Required: .IP \fB\-\-query_NAST\fR multi\-fasta file containing query sequences in alignment format .IP \fB\-\-db_NAST\fR db in NAST format .IP \fB\-\-db_FASTA\fR db in fasta format (megablast formatted) .SS Common options .IP \fB\-n\fR number of top matching database sequences to compare to (default 15) .IP \fB\-R\fR min divergence ratio default: 1.007 .IP \fB\-P\fR min percent identity among matching sequences (default 90) .SS Parameters to tune ChimeraMaligner: Scoring parameters: .IP \fB\-M\fR match score (default: +5) .IP \fB\-N\fR mismatch penalty (default: \fB\-4\fR) .IP \fB\-Q\fR min query coverage by matching database sequence (default: 70) .IP \fB\-T\fR maximum traverses of the multiple alignment (default: 1) .SS Flags: .IP \fB\-\-printAlignments\fR (default off) .IP \fB\-v\fR verbose .IP \fB\-\-exec_dir\fR cd here before running .SH "SEE ALSO" http://microbiomeutil.sourceforge.net/ .SH AUTHOR This manual page was written by Andreas Tille but can be freely used for any other distribution. debian/wigeon.manpages0000644000000000000000000000004612153401365012173 0ustar debian/wigeon.1 debian/cm_to_wigeon.1 debian/chimeraslayer.manpages0000644000000000000000000000002712153372026013533 0ustar debian/chimeraslayer.1 debian/nast-ier.install0000644000000000000000000000002112153326517012276 0ustar NAST-iEr usr/lib debian/wigeon.install0000644000000000000000000000001712153326335012047 0ustar WigeoN usr/lib debian/wigeon.10000644000000000000000000000310612153400235010533 0ustar .TH WIGEON "1" "June 2013" "wigeon " "User Commands" .SH NAME wigeon \- reimplementation of the Pintail 16S DNA anomaly detection utility .SH DESCRIPTION WigeoN examines the sequence conservation between a query and a trusted reference sequence, both in NAST alignment format. Based on the sequence identity between the query and the reference sequence, there is an expected amount of variation among the alignment. If the observed variation is greater than the 95% quantile of the distribution of variation observed between non-anomalous sequences, then it is flagged as an anomaly. .PP WigeoN is a flexible command-line based reimplementation of the Pintail algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36. .PP WigeoN is useful for flagging chimeras and anomalies only in near full-length 16S rRNA sequences. WigeoN lacks sensitivity with sequences less than 1000 bp. .PP To run WigeoN, you need NAST-formatted sequences generated by the nast-ier utility. .PP WigeoN is part of the microbiomeutil suite. .SH OPTIONS .SS Required: .IP \fB\-\-query_NAST\fR multi\-fasta file containing query sequences in alignment format .SS Optional: .IP \fB\-\-db_NAST\fR db in NAST format .IP \fB\-\-db_FASTA\fR db in fasta format (megablast formatted) .IP \fB\-\-num_top_hits\fR default 1: uses only the single best match. .IP \fB\-\-plot\fR .IP \fB\-\-DEBUG\fR .IP \fB\-\-exec_dir\fR cd to exec_dir before running .PP .SH "SEE ALSO" http://microbiomeutil.sourceforge.net/#A_WigeoN .SH AUTHOR This manual page was written by Andreas Tille but can be freely used for any other distribution. debian/rules0000755000000000000000000000242612173162713010255 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ #Kill the tests just now - they take too long. override_dh_auto_test : true override_dh_auto_build : dh_auto_build #Pre-make indexes for ChimeraSlayer, otherwise it tries to write them #to the non-writeable dir on first run and blows up formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta override_dh_auto_clean: dh_auto_clean rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log override_dh_install: dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c override_dh_fixperms : dh_fixperms find debian -type f -name '*.pm' -print0 | xargs -0r chmod a-x find debian -type f -name 'genus_counter.pl' -print0 | xargs -0r chmod a+x override_dh_builddeb: dh_builddeb -- -Z xz # 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 get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --repack-compression xz --destdir ../tarballs debian/watch0000644000000000000000000000014412173163657010231 0ustar version=3 opts="dversionmangle=s/\+dfsg//g" \ http://sf.net/microbiomeutil/microbiomeutil_(.*)\.tgz debian/upstream0000644000000000000000000000127512153330771010760 0ustar Reference: Author: Brian J. Haas and Dirk Gevers and Ashlee M. Earl and Mike Feldgarden and Doyle V. Ward and Georgia Giannoukos and Dawn Ciulla and Diana Tabbaa and Sarah K. Highlander and Erica Sodergren and Barbara Methé and Todd Z. DeSantis and The Human Microbiome Consortium and Joseph F. Petrosino and Rob Knight and Bruce W. Birren Title: "Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons" Journal: Genome Research Year: 2011 Volume: 21 Number: 3 Pages: 494-504 DOI: 10.1101/gr.112730.110 PMID: 21212162 URL: http://genome.cshlp.org/content/21/3/494.abstract eprint: http://genome.cshlp.org/content/21/3/494.full.pdf+html debian/copyright0000644000000000000000000000352312173161543011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Brian J. Haas Source: http://microbiomeutil.sourceforge.net/ Files-Excluded: docs/images Files: * Copyright: © 2009-2010 The Broad Institute License: BSD-like Files: debian/* Copyright: © 2010 Steffen Moeller © 2011-2013 Tim Booth © 2013 Andreas Tille License: BSD-like License: BSD-like * 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 Broad Institute 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 BROAD INSTITUTE ''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 BROAD INSTITUTE 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. debian/source/0000755000000000000000000000000012173163215010467 5ustar debian/source/format0000644000000000000000000000001411500166521011671 0ustar 3.0 (quilt) debian/nast-ier.manpages0000644000000000000000000000002212153375573012432 0ustar debian/nast-ier.1 debian/changelog0000644000000000000000000000510712173164657011057 0ustar microbiomeutil (20101212+dfsg-1) unstable; urgency=low * Initial release to Debian (Closes: #711086) * Remove copyrighted logo images from upstream tarball (the logo is only used in very short doc which works perfectly without this image) * debian/control: Use anonscm Vcs addresses -- Andreas Tille Mon, 22 Jul 2013 09:57:45 +0200 microbiomeutil (20101212-1ubuntu8) precise; urgency=low * Bio-Linux rebuild with Andreas' fixes * ChimeraSlayer run from QIIME was not working. Need to pre-compute index files and add them to RESOURCES directory * Also added missing direct dep on blast2 -- Tim Booth Wed, 05 Jun 2013 12:50:22 +0100 microbiomeutil (20101212-2) unstable; urgency=low * debian/copyright: DEP5 copyright * debian/control: - Added myself to uploaders - Priority: optional (as per Debian Med policy) - Droped DM-Upload-Allowed - Standards-Version: 3.9.4 - Debhelper 9 (also d/compat) - Dropped explicit quilt Build-Dependends - better formatting - Enhance long descriptions * debian/rules: - remove "--with quilt" because this is specified in source format - Use xz compression for binaries * debian/rules, debian/*.install, debian/*.links: Rather use the usual debhelper input files * Remove unneeded debian/README.* files and create debian/upstream file with citation information * Removed debian/{ChimeraSlayer,microbiomeutil.install} because unneeded * debian/*.1: Wrote manpages * debian/microbiomeutil.links: Synonyms with camel case spelling as in the provided documentation * debian/patches/hardening.patch: Enable propagation of hardening options -- Andreas Tille Tue, 04 Jun 2013 10:35:17 +0200 microbiomeutil (20101212-1ubuntu6) lucid; urgency=low * Another patch needed to Perl code due to inappropriate use of FindBin * Move to /usr/lib rather than /usr/share as per Lintian warnings. * Set --with quilt on dh. (Possibly not needed now?) * Added better descriptions in debian/control -- Tim Booth Mon, 03 Jun 2013 16:44:30 +0100 microbiomeutil (20101212-1ubuntu1) lucid; urgency=low * Split package into 4 binary packages. -- Tim Booth Mon, 11 Apr 2011 17:04:36 +0100 microbiomeutil (2010-11-1) UNRELEASED; urgency=low * New upstream -- Steffen Moeller Wed, 30 Mar 2011 00:23:15 +0200 microbiomeutil (2010-11-02-1) UNRELEASED; urgency=low * Initial packaging -- Steffen Moeller Thu, 02 Dec 2010 09:39:26 +0100 debian/patches/0000755000000000000000000000000012173165076010625 5ustar debian/patches/find_relocated_resources.patch0000644000000000000000000000351612173165076016707 0ustar Author: Tim Booth Description: Adapt path of some resources to Debian installation --- a/ChimeraSlayer/ChimeraSlayer.pl +++ b/ChimeraSlayer/ChimeraSlayer.pl @@ -11,8 +11,8 @@ use CdbTools; use File::Basename; -my $db_NAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; -my $db_FASTA = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.fasta"; +my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; +my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"; my $usage = <<_EOUSAGE_; --- a/ChimeraSlayer/util/CS_add_taxonomy.pl +++ b/ChimeraSlayer/util/CS_add_taxonomy.pl @@ -13,7 +13,7 @@ my %acc_to_taxonomy; { - my $fasta_reader = new Fasta_reader("$FindBin::Bin/../../RESOURCES/rRNA16S.gold.fasta"); + my $fasta_reader = new Fasta_reader("/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"); while (my $seq_obj = $fasta_reader->next()) { my $acc = $seq_obj->get_accession; --- a/NAST-iEr/run_NAST-iEr.pl +++ b/NAST-iEr/run_NAST-iEr.pl @@ -12,8 +12,8 @@ use Nuc_translator; -my $db_FASTA = "$FindBin::Bin/..//RESOURCES/rRNA16S.gold.fasta"; -my $db_NAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; +my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"; +my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; my $usage = <<_EOUSAGE_; --- a/WigeoN/run_WigeoN.pl +++ b/WigeoN/run_WigeoN.pl @@ -12,8 +12,8 @@ use CdbTools; -my $refDB = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.fasta"; -my $refNAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; +my $refDB = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"; +my $refNAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; my $usage = <<__EOUSAGE__; debian/patches/fix_perl_interpreter.patch0000644000000000000000000000146412173165024016077 0ustar Author: Tim Booth Description: Remove wrong or fix perl interpreter location --- a/NAST-iEr/PerlLib/Fasta_reader.pm +++ b/NAST-iEr/PerlLib/Fasta_reader.pm @@ -1,5 +1,3 @@ -#!/usr/local/bin/perl -w - # lightweight fasta reader capabilities: package Fasta_reader; --- a/ChimeraSlayer/PerlLib/Fasta_reader.pm +++ b/ChimeraSlayer/PerlLib/Fasta_reader.pm @@ -1,5 +1,3 @@ -#!/usr/local/bin/perl -w - # lightweight fasta reader capabilities: package Fasta_reader; --- a/WigeoN/PerlLib/Fasta_reader.pm +++ b/WigeoN/PerlLib/Fasta_reader.pm @@ -1,5 +1,3 @@ -#!/usr/local/bin/perl -w - # lightweight fasta reader capabilities: package Fasta_reader; --- a/RESOURCES/genus_counter.pl +++ b/RESOURCES/genus_counter.pl @@ -1,4 +1,4 @@ -#!/usr/bin/env perl +#!/usr/bin/perl use strict; use warnings; debian/patches/hardening.patch0000644000000000000000000000053212153375445013606 0ustar Author: Andreas Tille LastChanged: Tue, 04 Jun 2013 10:35:17 +0200 Description: Enable propagation of hardening options --- a/NAST-iEr/Makefile +++ b/NAST-iEr/Makefile @@ -3,7 +3,7 @@ all: NAST-iEr NAST-iEr: NAST-iEr.c - gcc NAST-iEr.c -o NAST-iEr + gcc $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) NAST-iEr.c -o NAST-iEr clean: debian/patches/series0000644000000000000000000000015112153375057012037 0ustar fix_perl_interpreter.patch find_relocated_resources.patch find_relocated_libraries.patch hardening.patch debian/patches/Makefile_make_no_NAST.patch0000644000000000000000000000117111500166521015666 0ustar Index: microbiomeutil-2010-11-02/Makefile =================================================================== --- microbiomeutil-2010-11-02.orig/Makefile 2010-12-02 09:55:58.332519690 +0100 +++ microbiomeutil-2010-11-02/Makefile 2010-12-02 09:57:32.116519685 +0100 @@ -1,5 +1,6 @@ -DIRS = NAST-iEr ChimeraSlayer WigeoN RESOURCES +#DIRS = NAST-iEr ChimeraSlayer WigeoN RESOURCES +DIRS = ChimeraSlayer WigeoN RESOURCES all clean: X=`pwd`; \ @@ -8,7 +9,8 @@ -test: testNast testWigeon testChimeraSlayer +#test: testNast testWigeon testChimeraSlayer +test: testWigeon testChimeraSlayer testNast: cd NAST-iEr; make test debian/patches/find_relocated_libraries.patch0000644000000000000000000000342012153361007016631 0ustar # Due to liberal use of FindBin, ChimeraSlayer can't be run from a symlink. # So I'm hard-coding the location to get around this. # Patch added by Tim Booth, see changelog --- a/ChimeraSlayer/ChimeraSlayer.pl +++ b/ChimeraSlayer/ChimeraSlayer.pl @@ -4,7 +4,9 @@ use warnings; use Getopt::Long qw(:config no_ignore_case bundling); -use FindBin; +#use FindBin; +#Hack needed because FindBin is braindead. +BEGIN{ $FindBin::Bin = "/usr/lib/ChimeraSlayer" }; use lib ("$FindBin::Bin/PerlLib"); use Fasta_reader; --- a/NAST-iEr/run_NAST-iEr.pl +++ b/NAST-iEr/run_NAST-iEr.pl @@ -5,7 +5,9 @@ use Getopt::Long; -use FindBin; +#use FindBin; +##Hack needed because FindBin is braindead. +BEGIN{ $FindBin::Bin = "/usr/lib/NAST-iEr" }; use lib ("$FindBin::Bin/PerlLib"); use Fasta_reader; use CdbTools; --- a/WigeoN/WigeoN.pl +++ b/WigeoN/WigeoN.pl @@ -5,7 +5,9 @@ use Carp; use Getopt::Long qw(:config no_ignore_case bundling); -use FindBin; +#use FindBin; +#Hack needed because FindBin is braindead. +BEGIN{ $FindBin::Bin = "/usr/lib/WigeoN" }; use POSIX; use lib ("$FindBin::Bin/PerlLib"); --- a/WigeoN/run_CM_to_WigeoN.pl +++ b/WigeoN/run_CM_to_WigeoN.pl @@ -4,9 +4,11 @@ use warnings; use Getopt::Long qw(:config no_ignore_case bundling); -use FindBin; +#use FindBin; +#Hack needed because FindBin is braindead. +BEGIN{ $FindBin::Bin = "/usr/lib/WigeoN" }; -use lib ("$FindBin::Bin/../PerlLib"); +use lib ("$FindBin::Bin/PerlLib"); use Fasta_reader; use CdbTools; --- a/WigeoN/run_WigeoN.pl +++ b/WigeoN/run_WigeoN.pl @@ -5,7 +5,9 @@ use Carp; use Getopt::Long qw(:config no_ignore_case bundling); -use FindBin; +#use FindBin; +#Hack needed because FindBin is braindead. +BEGIN{ $FindBin::Bin = "/usr/lib/WigeoN" }; use lib ("$FindBin::Bin/PerlLib"); use Fasta_reader; debian/chimeraslayer.install0000644000000000000000000000002612153326123013402 0ustar ChimeraSlayer usr/lib debian/compat0000644000000000000000000000000212153323460010363 0ustar 9 debian/nast-ier.links0000644000000000000000000000006212153326531011751 0ustar usr/lib/NAST-iEr/run_NAST-iEr.pl usr/bin/nast-ier debian/wigeon.links0000644000000000000000000000014512153326366011527 0ustar usr/lib/WigeoN/run_WigeoN.pl usr/bin/wigeon usr/lib/WigeoN/run_CM_to_WigeoN.pl usr/bin/cm_to_wigeon