Merge tag 'debian/3.6.2+dfsg-1' into debian/jessie-backports
roary Debian release 3.6.2+dfsg-1
Afif Elghraoui
7 years ago
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If the installation fails please contact your system administrator. If you encounter a bug please let us know by emailing roary@sanger.ac.uk .
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##Ubuntu/Debian
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All the dependancies can be installed using apt and cpanm (tested on Ubuntu 14.04). Root permissions are required.
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### Ubuntu 16.04
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```
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sudo apt-get install roary
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```
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###Ubuntu 14.04
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All the dependancies can be installed using apt and cpanm. Root permissions are required.
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```
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sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft fasttree
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sudo cpanm -f Bio::Roary
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```
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```
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###Ubuntu 12.04
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Some of the software versions in apt are quite old so follow the instructions for [LinuxBrew](http://brew.sh/linuxbrew/) below.
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roary (3.6.2+dfsg-1) unstable; urgency=medium
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* New upstream release.
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* Drop patches applied by upstream.
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-- Sascha Steinbiss <sascha@steinbiss.name> Tue, 10 May 2016 21:30:25 +0000
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roary (3.6.1+dfsg-2~bpo8+1) jessie-backports; urgency=medium
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* Rebuild for jessie-backports.
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The original code triggered a warning message in newer log4perl
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versions, breaking the autopkgtest.
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Author: Sascha Steinbiss <sascha@steinbiss.name>
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Forwarded: https://github.com/sanger-pathogens/Roary/pull/246
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--- a/lib/Bio/Roary/CommandLine/Common.pm
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+++ b/lib/Bio/Roary/CommandLine/Common.pm
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@@ -19,7 +19,7 @@
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rename_R_script.patch
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fix_log_message.patch
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name = Bio-Roary
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version = 3.6.1
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version = 3.6.2
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author = Andrew J. Page <ap13@sanger.ac.uk>
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license = GPL_3
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copyright_holder = Wellcome Trust Sanger Institute
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sub _build_logger
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{
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my ($self) = @_;
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Log::Log4perl->easy_init(level => $ERROR);
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Log::Log4perl->easy_init($ERROR);
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my $logger = get_logger();
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return $logger;
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}
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};
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no Moose;
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1;⏎
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1;
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Bio::Roary::Exceptions::FileNotFound->throw( error => "Cant find blast results: " . $output_file )
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unless ( -e $output_file );
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}
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my $output_files_param = join( ' ', @{$output_files} );
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system( "cat $output_files_param > " . $self->blast_results_file_name );
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if ( -e $self->blast_results_file_name )
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{
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system( "rm " . $self->blast_results_file_name );
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}
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system( "touch " . $self->blast_results_file_name );
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for my $output_file ( @{$output_files} ) {
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system( "cat $output_file >> " . $self->blast_results_file_name );
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}
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return 1;
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}
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