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commit 80536c8d5a983b870a6d5124e8d4feb05de1c666 Author: Sascha Steinbiss <[email protected]> Date: Mon Jan 15 13:40:19 2018 +0100 New upstream version 3.11.3+dfsg --- README.md | 5 ++--- dist.ini | 2 +- install_dependencies.sh | 2 +- lib/Bio/Roary/CommandLine/Roary.pm | 17 +++++++++++++++-- lib/Bio/Roary/External/CheckTools.pm | 20 +++++++++++--------- lib/Bio/Roary/ExtractProteomeFromGFF.pm | 9 +++++++-- lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm | 7 ++++++- 7 files changed, 43 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index e65364c..823f49a 100644 --- a/README.md +++ b/README.md @@ -69,9 +69,8 @@ sudo cpanm -f Bio::Roary ``` ## GNU Guix -Roary is not included in version in [Guix](https://www.gnu.org/software/guix) 0.11.0 so `guix pull` is currently required before installation. +Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way: ``` -guix pull guix package --install roary ``` @@ -130,7 +129,7 @@ The code will not work with perl 5.8 or below (pre-modern perl). We no longer te * cdhit 4.6.1 * ncbi blast+ 2.4.0 * mcl 14-137 -* bedtools 2.26.0 +* bedtools 2.27.1 * prank 130410 * GNU parallel 20130922, 20160722, 20150122 * FastTree 2.1.9 diff --git a/dist.ini b/dist.ini index e673cd7..1839c8f 100644 --- a/dist.ini +++ b/dist.ini @@ -3,7 +3,7 @@ author = Andrew J. Page <[email protected]> license = GPL_3 copyright_holder = Wellcome Trust Sanger Institute copyright_year = 2013 -version = 3.11.0 +version = 3.11.3 main_module = lib/Bio/Roary.pm [MetaResources] diff --git a/install_dependencies.sh b/install_dependencies.sh index 253ed7b..bdc0256 100755 --- a/install_dependencies.sh +++ b/install_dependencies.sh @@ -11,7 +11,7 @@ PARALLEL_VERSION=${PARALLEL_VERSION:-"20160722"} PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2" PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}"; -BEDTOOLS_VERSION="2.26.0" +BEDTOOLS_VERSION="2.27.1" BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz" BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}"; diff --git a/lib/Bio/Roary/CommandLine/Roary.pm b/lib/Bio/Roary/CommandLine/Roary.pm index e2335a0..a98610c 100644 --- a/lib/Bio/Roary/CommandLine/Roary.pm +++ b/lib/Bio/Roary/CommandLine/Roary.pm @@ -21,6 +21,7 @@ use File::Which; use File::Path qw(make_path); use Cwd qw(abs_path getcwd); use File::Temp; +use File::Basename; extends 'Bio::Roary::CommandLine::Common'; has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); @@ -120,7 +121,7 @@ sub BUILD { Pubmed: 26198102\n\n"; $self->help($help) if ( defined($help) ); - if( $self->help ) + if( $self->help ) { print $self->usage_text; return; @@ -141,6 +142,18 @@ sub BUILD { $self->logger->error("Error: You need to provide at least 2 files to build a pan genome"); die $self->usage_text; } + my %basenames; + foreach my $string (@{$self->args}) { + my($base, $path, $suf) = fileparse($string); + next unless $basenames{$base}++; + $self->logger->error("Error: GFF files must have unique basenames."); + die $self->usage_text; + } + + if ( @{ $self->args } < 2 ) { + $self->logger->error("Error: You need to provide at least 2 files to build a pan genome"); + die $self->usage_text; + } $self->output_filename($output_filename) if ( defined($output_filename) ); $self->job_runner($job_runner) if ( defined($job_runner) ); $self->makeblastdb_exec($makeblastdb_exec) if ( defined($makeblastdb_exec) ); @@ -246,7 +259,7 @@ sub _setup_output_directory { sub run { my ($self) = @_; - + return if($self->version || $self->help); $self->_setup_output_directory; diff --git a/lib/Bio/Roary/External/CheckTools.pm b/lib/Bio/Roary/External/CheckTools.pm index dc01fd5..1a73cf5 100644 --- a/lib/Bio/Roary/External/CheckTools.pm +++ b/lib/Bio/Roary/External/CheckTools.pm @@ -57,28 +57,30 @@ my %tools = ( }, 'mafft' => { GETVER => "mafft --version < /dev/null 2>&1", - REGEXP => qr/(\d+\.\d+) /, + REGEXP => qr/(\d+\.\d+)/, NEEDED => 1, }, 'kraken' => { - GETVER => "kraken --version | head -n 1", - REGEXP => qr/(\d+\.\d+\.\d+.*)/, + GETVER => "kraken -v | head -n 1", + REGEXP => qr/(\d+\.\d+\.*\d*.*)/, NEEDED => 0, }, 'kraken-report' => { - GETVER => "kraken-report --version | head -n 1", - REGEXP => qr/(\d+\.\d+\.\d+.*)/, + GETVER => "kraken-report -v | head -n 1", + REGEXP => qr/(\d+\.\d+\.*\d*.*)/, NEEDED => 0, - }, + }, 'Rscript' => { GETVER => "Rscript --version 2>&1 | head -n 1", REGEXP => qr/R scripting front-end version ($BIDEC)/, MINVER => "3", NEEDED => 0, }, - - # prank version also performs an update check so cant use it - 'prank' => { NEEDED => 0 }, + 'prank' => { + GETVER => "prank | grep -m 1 ^prank", + REGEXP => qr/prank v.(\d+)/, + NEEDED => 0, + }, # now just the standard unix tools we need 'grep' => { NEEDED => 1 }, diff --git a/lib/Bio/Roary/ExtractProteomeFromGFF.pm b/lib/Bio/Roary/ExtractProteomeFromGFF.pm index 8940aed..a96e087 100644 --- a/lib/Bio/Roary/ExtractProteomeFromGFF.pm +++ b/lib/Bio/Roary/ExtractProteomeFromGFF.pm @@ -132,8 +132,13 @@ sub _cleanup_fasta { open( my $in, '<', $infile ); open( my $out, '>', $outfile ); while ( my $line = <$in> ) { - chomp $line; - $line =~ s/"//g if ( $line =~ /^>/ ); + chomp $line; + if ( $line =~ /^>/ ) + { + $line =~ s/"//g; + # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them + $line =~ s!\([-+]\)!!; + } if($line =~ /^(>[^:]+)/) { diff --git a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm index 14413dc..2a16b1a 100644 --- a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm +++ b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm @@ -177,7 +177,12 @@ sub _cleanup_fasta { open( my $out, '>', $outfile ); while ( my $line = <$in> ) { chomp $line; - $line =~ s/"//g if ( $line =~ /^>/ ); + if ( $line =~ /^>/ ) + { + $line =~ s/"//g ; + # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them + $line =~ s!\([-+]\)!!; + } if($line =~ /^(>[^:]+)/) { -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
