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commit af9817c6ca0b18b1b59026525697798a76a24330 Author: Sascha Steinbiss <[email protected]> Date: Sun Jan 21 23:46:06 2018 +0100 New upstream version 3.11.4+dfsg --- README.md | 29 ++++++++--------------------- dist.ini | 2 +- lib/Bio/Roary/CommandLine/Roary.pm | 21 ++++++++++++++------- 3 files changed, 23 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index 823f49a..fb94f70 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,6 @@ Theres are a number of dependancies required for Roary, with instructions specif * CentOS/RedHat * Bioconda - OSX/Linux * Galaxy -* Homebrew/Linuxbrew - OSX/Linux * Guix - Linux * Virtual Machine - OSX/Linux/Windows * Docker - OSX/Linux/Windows/Cloud @@ -40,10 +39,7 @@ sudo cpanm -f Bio::Roary ``` ### Ubuntu 12.04 -Some of the software versions in apt are quite old so follow the instructions for [LinuxBrew](http://brew.sh/linuxbrew/) below. - -## CentOS/RedHat -To install the dependancies, the easiest way is to install [LinuxBrew](http://brew.sh/linuxbrew/) using the steps for Fedora, then follow the steps below for installing Roary on LinuxBrew. +Some of the software versions in apt are quite old so follow the instructions for Bioconda below. ## Bioconda - OSX/Linux Install conda. Then install bioconda and roary: @@ -57,16 +53,7 @@ conda install roary ``` ## Galaxy -Roary is available from the Galaxy toolshed ( as is Prokka). - -## Homebrew/Linuxbrew - OSX/Linux -Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.sh/linuxbrew/) (Linux) setup and installed on your system: - -``` -brew tap homebrew/science -brew install bedtools cd-hit blast mcl parallel prank mafft fasttree cpanm -sudo cpanm -f Bio::Roary -``` +Roary is available from the Galaxy toolshed ( as is Prokka ). ## GNU Guix Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way: @@ -122,14 +109,14 @@ bedtools cd-hit blast mcl GNUparallel prank mafft fasttree ``` ## Ancient systems and versions of perl -The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007). If you're running a very old verison of Linux, you're also in trouble. +The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007) or 5.12 (released 2010). If you're running a very old verison of Linux, you're also in trouble. # Versions of software we test against -* Perl 5.14, 5.16, 5.20, 5.24 -* cdhit 4.6.1 -* ncbi blast+ 2.4.0 +* Perl 5.14, 5.26 +* cdhit 4.6.8 +* ncbi blast+ 2.6.0 * mcl 14-137 * bedtools 2.27.1 -* prank 130410 -* GNU parallel 20130922, 20160722, 20150122 +* prank 140603 +* GNU parallel 20170822, 20160722 * FastTree 2.1.9 diff --git a/dist.ini b/dist.ini index 1839c8f..2f0cae1 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 = 3.11.3 +version = 3.11.4 main_module = lib/Bio/Roary.pm [MetaResources] diff --git a/lib/Bio/Roary/CommandLine/Roary.pm b/lib/Bio/Roary/CommandLine/Roary.pm index a98610c..78ce692 100644 --- a/lib/Bio/Roary/CommandLine/Roary.pm +++ b/lib/Bio/Roary/CommandLine/Roary.pm @@ -42,6 +42,7 @@ has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 ); has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'perc_identity' => ( is => 'rw', isa => 'Num', default => 95 ); has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 ); +has 'check_dependancies' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 ); has 'dont_run_qc' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'dont_split_groups' => ( is => 'rw', isa => 'Bool', default => 0 ); @@ -126,16 +127,22 @@ sub BUILD { print $self->usage_text; return; } + + if ( defined($verbose) ) { + $self->verbose($verbose); + $self->logger->level(10000); + } - if ($check_dependancies) { + $self->check_dependancies($check_dependancies) if ( defined($check_dependancies) ); + if ($self->check_dependancies) { my $check_tools = Bio::Roary::External::CheckTools->new(); $check_tools->check_all_tools; $self->logger->error( "Roary version " . $self->_version() ); - } - - if ( defined($verbose) ) { - $self->verbose($verbose); - $self->logger->level(10000); + + if( @{ $self->args } < 1 ) + { + return; + } } if ( @{ $self->args } < 2 ) { @@ -260,7 +267,7 @@ sub _setup_output_directory { sub run { my ($self) = @_; - return if($self->version || $self->help); + return if($self->version || $self->help || ($self->check_dependancies && @{$self->fasta_files} < 1) ); $self->_setup_output_directory; -- 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
