debian/0000755000000000000000000000000012241376352007173 5ustar debian/control0000644000000000000000000000700612241376257010605 0ustar Source: bioperl-run Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Build-Depends-Indep: perl, bioperl (>= 1.6.9), # Recommended in Build.PL: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, # Not yet available: libfile-sort-perl # Needed for the tests, but not documented Upstream libarray-compare-perl, libtree-dagnode-perl, # Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup. # amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, # hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons, # samtools, sim4, t-coffee, tigr-glimmer, wise, # Needed for the network tests: libwww-perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bioperl-run/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bioperl-run/trunk/ Homepage: http://www.bioperl.org/wiki/Run_package Package: bioperl-run Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, bioperl, libbio-perl-run-perl (= ${source:Version}) Recommends: amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probalign, probcons, samtools, sim4, t-coffee, tigr-glimmer, wise Suggests: # Non-Free. gmap, paml, # Removed from Debian at all molphy, # Removed from Debian but might be reintroduced ensembl, phylip # The following list of packages is not available in Debian: # blat, # cap3, # coils, # condense, # drawgram, # drawtree, # eponine, # fasta, # non-free, inofficial package for BioLinux # footprinter, # genemark-hmm, # genscan, # gerp, # glimmer2, # hyphy, # lagan, # packaging work in progress # lvb, # match, # mcs, # mdust, # meme, # non-free, packaging work in progress # minimo, # neighbor, # newbler, # njtree, # pal2nal, # phastcons, # phrap, # primate, # prints, # profile, # promoterwise, # protdist, # protpars, # pseudowise, # quikctree, # repeatmasker, # sablastplus, # seg, # semphy, # seqboot, # signalp, # simprot, # slr, # soapeu, # tigr-assembler, # tmhmm, # tribe, # trnascan, # vista-align Description: BioPerl wrappers: scripts Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package. Package: libbio-perl-run-perl Architecture: all Section: perl Depends: ${misc:Depends}, ${perl:Depends}, libbio-perl-perl Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libwww-perl Breaks: bioperl-run (<< 1.6.9) Replaces: bioperl-run (<< 1.6.9) Description: BioPerl wrappers: modules Contains modules that provide a Perl interface to various bioinformatics applications to allow them to be used with common BioPerl objects. debian/rules0000755000000000000000000000035412241370572010253 0ustar #!/usr/bin/make -f ifneq (,$(DEB_MAINTAINER_MODE)) NETWORK = --network endif %: dh $@ override_dh_auto_configure: dh_auto_configure -- --install_scripts $(NETWORK) override_dh_auto_test: # PATH=$$PATH:/usr/lib/emboss dh_auto_test debian/watch0000644000000000000000000000040212241373011010205 0ustar version=3 opts="uversionmangle=s/_/./g" \ https://github.com/bioperl/bioperl-run/releases .*/archive/release-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$ # http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/bioperl-run.install0000644000000000000000000000003312214301073013001 0ustar usr/bin usr/share/man/man1 debian/copyright0000644000000000000000000000615712241370735011136 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz Files: * Copyright: © 1997–2011 Bioperl Team Sendu Bala Jer-Ming Chia Rob Edwards Mauricio Herrera Cuadra Shawn Hoon Donald Jackson Keith James Ratnapu Kiran Kumar Balamurugan Kumarasamy Catherine Letondal Heikki Lehvaslaiho Stephen Montgomery Brian Osborne Tania Oh Peter Schattner Martin Senger Marc Sohrmann Jason Stajich Elia Stupka David Vilanova Albert Vilella Tiequan Zhang Juguang Xiao Comment: Everyone can use it! We don't care if you are academic, corporate, or government. BioPerl is licensed under the same terms as Perl itself, which means it is dually-licensed under either the Artistic or GPL licenses. The Perl Artistic License, or the GNU GPL covers all the legalese and what you can and can't do with the source code. . We do appreciate: . * You letting us know you sell or use a product that uses BioPerl. This helps us show people how useful our toolkit is. It also helps us if we seek funding from a government source, to identify the utility of the code to many different groups of users. Add your project and institution to our BioPerl Users page. . * If you fix bugs, please let us know about them. Because Bioperl is dual-licensed under the GPL or Artistic licenses, you can choose the Artistic license, which means that you are not required to submit the code fixes, but in the spirit of making a better product we hope you'll contribute back to the community any insight or code improvements. . * Please include the AUTHORS file and ascribe credit to the original BioPerl toolkit where appropriate. . * If you are an academic and you use the software, please cite the article. See the BioPerl publications for a list of papers which describe components in the toolkit. . See http://www.bioperl.org/wiki/Licensing_BioPerl License: Perl This program is free software; you can redistribute it and/or modify it under the terms of either: . a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or . b) the "Artistic License" which comes with Perl. . On Debian systems, the complete text of the Artistic License can be found in ‘/usr/share/common-licenses/Artistic’, and the complete text of the latest version of the GNU General Public License version 1 can be found in ‘/usr/share/common-licenses/GPL-1’. debian/source/0000755000000000000000000000000012214301073010457 5ustar debian/source/format0000644000000000000000000000001412214301073011665 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000261212214301073011221 0ustar bioperl-run for Debian ---------------------- (Extracted from the INSTALL file) ENVIRONMENT VARIABLES Some important environment variables you need to be aware of. Variable Values Comment -------------------------------------------------------------------- PHYLIPVERSION 3.5, 3.6 If you want to run Phylip3.6 you need to set this env variable to 3.6 BLASTDIR DIR PATH Point to the directory where BLAST is installed GENSCAN_DIR DIR PATH Point to the directory where HumanIso.smat file is installed EPONINEDIR DIR PATH Point to the directory where eponine_scan.jar is installed PAMLDIR DIR PATH Point to directory where PAML is installed Generally the all-caps program name concatenated to 'DIR' patten for environment variable names is followed for most programs. However there are some exceptions (some require an underscore between the program name and 'DIR'), so check the documentation for the module you're interested in using. Note that for some programs, having the executables in your path is not enough - the correct environment variable still needs to be set, and sometimes it shouldn't point to the executable location, but somewhere else - again, check the documentation. debian/README.test0000644000000000000000000000051612214301073011017 0ustar Some upstream regression tests require access to Internet ressources, so they are disabled by default as network connectivity is not guaranteed in the Debian build daemons. But it is very recommended to run them locally before uploading this package. To do this, set the DEB_MAINTAINER_MODE environment variable (see debian/rules). debian/changelog0000644000000000000000000000652512241376352011055 0ustar bioperl-run (1.6.9-2) unstable; urgency=low * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - canonical Vcs URLs - debhelper 9 * debian/README.source: removed because redundant * debian/copyright: DEP5 * debian/watch: Point download location to github which provides more reliable version numbering than CPAN which would have needed a more complex version mangling * refreshed quilt patches to get rid of fuzz -- Andreas Tille Fri, 15 Nov 2013 10:03:29 +0100 bioperl-run (1.6.9-1) unstable; urgency=low * New upstream release. * Converted and validated debian/copyright to latest machine-readable format. * debian/control: - Refreshed the list of packages for which wrappers are provided, in the Suggests field as well as in an experimental Build-Recommends field. - Incremented Standards-Version to reflect conformance with Policy 3.9.2. No other changes needed. - Vcs-Browser URL made redirectable to viewvc. - Removed useless ‘svn’ in the Vcs-Svn URL. * Point debian/watch to CPAN. * Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control). * Split scripts in bioperl-run and modules in libbio-perl-run-perl. (debian/rules, debian/control, debian/bioperl-run.install, debian/libbio-perl-run-perl.install) * debian/rules, debian/patches/series, debian/control: - debian/patches/install-scripts.patch for non-interactive script install. - debian/patches/Use-system-s-Perl.patch against /usr/local/bin/perl. - debian/patches/Some-spellchecking.patch. * Trigger network tests with DEB_MAINTAINER_MODE (debian/rules, debian/README.test). -- Charles Plessy Sat, 18 Jun 2011 13:21:36 +0900 bioperl-run (1.6.1-1) unstable; urgency=low * New upstream release. * debian/patches/10-wrong-path-for-interpreter.patch: removed (fixed upstream). * debian/watch updated (bioperl -> BioPerl). * debian/rules refreshed with dh-make-perl 0.53. - Disabled installation of examples (removed upstream). - Removed the correction of file permission of Pise documentation (removed upstream). - Removed patching facilities (no patches anymore). - Disabled tests as I experience failures with t/Eponine.t despite this program is not installed. * debian/copyright: - Removed vanity lines about debianization and debian copyright. - Incremented years to 2009. - Updated to latest experimentation of the machine-readable license summary. * debian/control: - Incremented Standards-Version to reflect conformance on new Policy (dropped versionned build-dependancy on Perl). - Removed build-dependancy on quilt (no patches anymore). - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0. - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl, libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES. - Build-depends on libarray-compare-perl and libtree-dagnode-perl (otherwise tests fail). - Depend on amap-align instead of amap (Closes: #541274). -- Charles Plessy Thu, 03 Sep 2009 11:00:03 +0900 bioperl-run (1.5.2.100-1) unstable; urgency=low * Initial Release (Closes: #505112). -- Charles Plessy Mon, 10 Nov 2008 09:11:17 +0900 debian/patches/0000755000000000000000000000000012241374304010615 5ustar debian/patches/Use-system-s-Perl.patch0000644000000000000000000000107212241374033015053 0ustar Forwarded: https://redmine.open-bio.org/issues/3255 From 8d4322bea521c457029a00155fe292ef7ef177d4 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Sat, 18 Jun 2011 12:58:08 +0900 Subject: [PATCH] Use system's Perl. --- scripts/bioperl_application_installer.PLS | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) --- a/scripts/bioperl_application_installer.PLS +++ b/scripts/bioperl_application_installer.PLS @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # BioPerl script for Bio::Installer # # Cared for by Albert Vilella debian/patches/install-scripts.patch0000644000000000000000000000232612241374304014774 0ustar Forwarded: https://redmine.open-bio.org/issues/3254 From 4d1fe98b390c67170d0d23325de5ccd8fdc6ea1a Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Sat, 18 Jun 2011 12:43:21 +0900 Subject: [PATCH] New --install_scripts option to request script installation non-interactively. --- Build.PL | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) --- a/Build.PL +++ b/Build.PL @@ -27,7 +27,8 @@ my $build = Module::Build->new( }, get_options => { accept => { }, - network => { } + network => { }, + install_scripts => { } }, auto_features => { Network => { @@ -42,7 +43,7 @@ my $build = Module::Build->new( my $accept = $build->args->{accept}; # Optionally have script files installed. -if ($accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) { +if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) { my $files = $build->_find_file_by_type('PLS', 'scripts'); my $script_build = File::Spec->catdir($build->blib, 'script'); debian/patches/Some-spellchecking.patch0000644000000000000000000003067212241374116015363 0ustar Forwarded: https://redmine.open-bio.org/issues/3256 From b6c1d10797c2fbb6c5fe3c0fe2e5f74d252889cb Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Sat, 18 Jun 2011 13:13:43 +0900 Subject: [PATCH] Some spellchecking. --- lib/Bio/Tools/Run/Alignment/Clustalw.pm | 2 +- lib/Bio/Tools/Run/Alignment/Pal2Nal.pm | 2 +- lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm | 2 +- lib/Bio/Tools/Run/AssemblerBase.pm | 2 +- lib/Bio/Tools/Run/FootPrinter.pm | 2 +- lib/Bio/Tools/Run/Hmmer.pm | 2 +- lib/Bio/Tools/Run/MCS.pm | 2 +- lib/Bio/Tools/Run/Phylo/Gerp.pm | 4 ++-- lib/Bio/Tools/Run/Phylo/Gumby.pm | 4 ++-- lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm | 2 +- lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm | 6 +++--- lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm | 4 ++-- lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm | 2 +- lib/Bio/Tools/Run/Phylo/Phyml.pm | 4 ++-- lib/Bio/Tools/Run/Phylo/QuickTree.pm | 2 +- lib/Bio/Tools/Run/Phylo/Semphy.pm | 4 ++-- lib/Bio/Tools/Run/StandAloneBlastPlus.pm | 2 +- lib/Bio/Tools/Run/TigrAssembler.pm | 2 +- t/lib/Test/Builder/Tester.pm | 2 +- 19 files changed, 26 insertions(+), 26 deletions(-) --- a/lib/Bio/Tools/Run/Alignment/Clustalw.pm +++ b/lib/Bio/Tools/Run/Alignment/Clustalw.pm @@ -205,7 +205,7 @@ clustalw program have not yet been imple that a specific clustalw feature be added to this perl contact bioperl-l@bioperl.org. -These can be specified as paramters when instantiating a new Clustalw +These can be specified as parameters when instantiating a new Clustalw object, or through get/set methods of the same name (lowercase). =head1 PARAMETER FOR ALIGNMENT COMPUTATION --- a/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm +++ b/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm @@ -192,7 +192,7 @@ sub new { Args : The first argument represents a protein alignment, the second argument a set of nucleotide sequences. The alignment can be provided as an alignment file readable by - Bio::AlignIO, or a Bio::Align::AlignI complient object (eg. a + Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The nucleotide sequences can be provided as a single filename of a fasta file containing multiple nucleotide sequences, or an array ref --- a/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm +++ b/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm @@ -117,7 +117,7 @@ Email tqzhang1973@yahoo.com =head1 Appendix The rest of the documendation details each of the object -methods. Internal methods are preceeded with a underscore +methods. Internal methods are preceded with a underscore =cut --- a/lib/Bio/Tools/Run/AssemblerBase.pm +++ b/lib/Bio/Tools/Run/AssemblerBase.pm @@ -865,7 +865,7 @@ sub parameters_changed { Usage : @params = $pobj->available_parameters() Function: Returns a list of the available parameters Returns : Array of parameters - Args : 'params' for settable program paramters + Args : 'params' for settable program parameters 'switches' for boolean program switches default: all --- a/lib/Bio/Tools/Run/FootPrinter.pm +++ b/lib/Bio/Tools/Run/FootPrinter.pm @@ -67,7 +67,7 @@ Written by Mathieu Blanchette and Martin =head2 Running Footprinter -To run FootPrinter, you will need to set the enviroment variable +To run FootPrinter, you will need to set the environment variable FOOTPRINTER_DIR to where the binary is located (even if the executable is in your path). For example: --- a/lib/Bio/Tools/Run/Hmmer.pm +++ b/lib/Bio/Tools/Run/Hmmer.pm @@ -172,7 +172,7 @@ our @UNSUPPORTED = qw(h verbose a -o is synonymous with -outfile # may be specified here, allowing run() to be used, or - # it can be ommitted and the corresponding method (eg. + # it can be omitted and the corresponding method (eg. # hmmalign()) used later. -program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch --- a/lib/Bio/Tools/Run/MCS.pm +++ b/lib/Bio/Tools/Run/MCS.pm @@ -216,7 +216,7 @@ sub new { third argument represents annotation of the exons in the alignment. The alignment can be provided as a multi-fasta format alignment - filename, or a Bio::Align::AlignI complient object (eg. a + filename, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The position in the genome can be provided as a Bio::Location::Atomic --- a/lib/Bio/Tools/Run/Phylo/Gerp.pm +++ b/lib/Bio/Tools/Run/Phylo/Gerp.pm @@ -211,10 +211,10 @@ sub new { Args : The first argument represents an alignment, the second argument a phylogenetic tree with branch lengths. The alignment can be provided as a MAF format alignment - filename, or a Bio::Align::AlignI complient object (eg. a + filename, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The species tree can be provided as a newick format tree filename - or a Bio::Tree::TreeI complient object. + or a Bio::Tree::TreeI compliant object. In all cases, the alignment sequence names must correspond to node ids in the tree. Multi-word species names should have the --- a/lib/Bio/Tools/Run/Phylo/Gumby.pm +++ b/lib/Bio/Tools/Run/Phylo/Gumby.pm @@ -284,10 +284,10 @@ sub annots { Args : The first argument represents an alignment, the second argument a species tree. The alignment can be provided as a multi-fasta format alignment - filename, or a Bio::Align::AlignI complient object (eg. a + filename, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The species tree can be provided as a newick format tree filename - or a Bio::Tree::TreeI complient object. Alternatively a + or a Bio::Tree::TreeI compliant object. Alternatively a Bio::DB::Taxonomy object can be supplied, in which case the species tree will be generated by using the alignment sequence names as species names and looking for those in the supplied database. --- a/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm +++ b/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm @@ -554,7 +554,7 @@ sub set_parameter{ Returns : none Args : boolean: keep existing parameter values NB : using this isn't an especially good idea! You don't need to do - anything to end up using default paramters: hence 'default'! + anything to end up using default parameters: hence 'default'! =cut --- a/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm +++ b/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm @@ -331,13 +331,13 @@ sub rho { ('footprinting'). Returns : array of Bio::SeqFeature::Annotated (one feature per alignment sequence and prediction) - Args : The first arguement represents an alignment, the second arguement + Args : The first argument represents an alignment, the second argument a species tree. The alignment can be provided as a multi-fasta format alignment - filename, or a Bio::Align::AlignI complient object (eg. a + filename, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The species tree can be provided as a newick format tree filename - or a Bio::Tree::TreeI complient object. Alternatively a + or a Bio::Tree::TreeI compliant object. Alternatively a Bio::DB::Taxonomy object can be supplied, in which case the species tree will be generated by using the alignment sequence names as species names and looking for those in the supplied database. --- a/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm +++ b/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm @@ -241,10 +241,10 @@ sub new { Args : The first argument represents an alignment, the second argument a species tree. The alignment can be provided as a multi-fasta format alignment - filename, or a Bio::Align::AlignI complient object (eg. a + filename, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The species tree can be provided as a newick format tree filename - or a Bio::Tree::TreeI complient object. Alternatively a + or a Bio::Tree::TreeI compliant object. Alternatively a Bio::DB::Taxonomy object can be supplied, in which case the species tree will be generated by using the alignment sequence names as species names and looking for those in the supplied database. --- a/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm +++ b/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm @@ -97,7 +97,7 @@ this is still experimental as v3.6 is st Title : TYPE Description : (optional) - Only avaliable in phylip v3.6 + Only available in phylip v3.6 This program supports 3 types of consensus generation --- a/lib/Bio/Tools/Run/Phylo/Phyml.pm +++ b/lib/Bio/Tools/Run/Phylo/Phyml.pm @@ -315,7 +315,7 @@ sub version { Returns : Bio::Tree::Tree object Args : file name for your input alignment in a format recognised by AlignIO, OR Bio::Align::AlignI - complient object (eg. Bio::SimpleAlign). + compliant object (eg. Bio::SimpleAlign). =cut @@ -358,7 +358,7 @@ sub stats { Title : tree_string Usage : $factory->tree_string; $factory->run($align_object); - Function: Returns the contents of the phyml '_phyml_tree.txt' ouput file + Function: Returns the contents of the phyml '_phyml_tree.txt' output file Returns : string with tree in Newick format, undef before run() Args : none --- a/lib/Bio/Tools/Run/Phylo/QuickTree.pm +++ b/lib/Bio/Tools/Run/Phylo/QuickTree.pm @@ -240,7 +240,7 @@ sub boot { Function: Runs QuickTree to generate a tree Returns : Bio::Tree::Tree object Args : file name for your input alignment in stockholm format, OR - Bio::Align::AlignI complient object (eg. Bio::SimpleAlign). + Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign). =cut --- a/lib/Bio/Tools/Run/Phylo/Semphy.pm +++ b/lib/Bio/Tools/Run/Phylo/Semphy.pm @@ -252,10 +252,10 @@ sub new { argument a species tree (to set an initial tree: normally the -t option to Semphy). The alignment can be provided as a multi-fasta format alignment - filename, or a Bio::Align::AlignI complient object (eg. a + filename, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign). The species tree can be provided as a newick format tree filename - or a Bio::Tree::TreeI complient object. Alternatively a + or a Bio::Tree::TreeI compliant object. Alternatively a Bio::DB::Taxonomy object can be supplied, in which case the species tree will be generated by using the alignment sequence names as species names and looking for those in the supplied database. --- a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm +++ b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm @@ -210,7 +210,7 @@ To get the tempfile basename, do: =item * Specify data post-construction -Use the explict attribute setters: +Use the explicit attribute setters: $fac = Bio::Tools::Run::StandAloneBlastPlus->new( -create => 1 --- a/lib/Bio/Tools/Run/TigrAssembler.pm +++ b/lib/Bio/Tools/Run/TigrAssembler.pm @@ -179,7 +179,7 @@ TIGR Assembler options available in this ignore_tandem_32mers: a flag which causes tandem 32mers (a tandem 32mer is a 32mer which occurs more than once in at least one sequence read) to be ignored (this is now the default behavior and this flag is for backward - compatability) + compatibility) use_tandem_32mers: a flag which causes tandem 32mers to be used for pairwise comparison opposite of the -t flag which is now the default). safe_merging_stop: a flag which causes merging to stop when only sequences --- a/t/lib/Test/Builder/Tester.pm +++ b/t/lib/Test/Builder/Tester.pm @@ -323,7 +323,7 @@ will function normally and cause success sub test_test { - # decode the arguements as described in the pod + # decode the arguments as described in the pod my $mess; my %args; if (@_ == 1) debian/patches/series0000644000000000000000000000010712214301073012021 0ustar install-scripts.patch Use-system-s-Perl.patch Some-spellchecking.patch debian/compat0000644000000000000000000000000212241370556010371 0ustar 9 debian/libbio-perl-run-perl.install0000644000000000000000000000004312214301073014506 0ustar usr/share/perl5 usr/share/man/man3