Merge pull request #97 from andrewjpage/master

Rename directories to Roary
sanger-pathogens · Mar 16, 2015 · a53c2f7 · a53c2f7
2 parents 7a5df58 + a52715c
commit a53c2f7
Show file tree

Hide file tree

Showing 133 changed files with 661 additions and 630 deletions.
diff --git a/.gitignore b/.gitignore
@@ -32,4 +32,5 @@ set_difference_unique_set_one_reannotated
 set_difference_unique_set_two_reannotated
 extras/
 bin/shred_assemblies
-Bio-PanGenome-*
+Bio-Roary-*
+Roary-*
diff --git a/README.md b/README.md
@@ -5,41 +5,41 @@ Roary is a high speed stand alone pan genome pipeline, which takes annotated ass
 ##Installation - The quick and dirty way
 
 ###Download
-Download the latest software from https://github.com/sanger-pathogens/Bio-Roary/archive/v2.0.0.tar.gz
+Download the latest software from 
+https://github.com/sanger-pathogens/Bio-Roary/archive/v2.0.0.tar.gz
 
 ###Extract
 
 Choose somewhere to put it, for example in your home directory (no root access required):
 
-  cd $HOME
-  tar zxvf Roary-XXXX.tar.gz
-  ls Roary*
+  `cd $HOME`
+  `tar zxvf Roary-XXXX.tar.gz`
+  `ls Roary*`
 
 ###Add to your Environment
 
 Add the following lines to your $HOME/.bashrc file, or to /etc/profile.d/roary.sh to make it available to all users:
 
-   export PATH=$PATH:$HOME/Bio-Roary-x.xxx/bin
-   export PERL5LIB=$PERL5LIB:$HOME/Bio-Roary-x.xxx/lib
+   `export PATH=$PATH:$HOME/Bio-Roary-x.xxx/bin`
+   `export PERL5LIB=$PERL5LIB:$HOME/Bio-Roary-x.xxx/lib`
 
 ###Install perl dependancies
-   cpanm Array::Utils BioPerl Exception::Class File::Find::Rule File::Grep File::Slurp Graph Moose Moose::Role Text::CSV
+   `cpanm Array::Utils BioPerl Exception::Class File::Find::Rule File::Grep File::Slurp Graph Moose Moose::Role Text::CSV`
 
 
 
 ##Installation - Ubuntu/Debian
 ###Install the dependancies
 Assuming you have root on your system, all the dependancies executables are installable using apt.
-   sudo apt-get install bedtools cd-hit ncbi-blast+ mcl muscle parallel
+   `sudo apt-get install bedtools cd-hit ncbi-blast+ mcl muscle parallel`
 
 ###Install Roary and its perl dependancies
-   cpanm Bio::Roary
-
+   `cpanm Bio::Roary`
 
 ##Installation - OSX using homebrew
 Assuming you have homebrew setup and installed on your OSX system tap the science keg and install the dependancies:
-   brew tap homebrew/science
-   brew install bedtools cd-hit blast mcl muscle parallel
+   `brew tap homebrew/science`
+   `brew install bedtools cd-hit blast mcl muscle parallel`
 
 ###Install Roary and its perl dependancies
-   cpanm Bio::Roary
+   `cpanm Bio::Roary`
diff --git a/bin/create_pan_genome b/bin/create_pan_genome
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::CreatePanGenome;
+package Bio::Roary::Main::CreatePanGenome;
 
 # ABSTRACT: Create a pan genome from a set of proteome FASTA files
 # PODNAME: create_pan_geneome
@@ -14,6 +14,6 @@ Create a pan genome from a set of proteome FASTA files
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::CreatePanGenome;
+use Bio::Roary::CommandLine::CreatePanGenome;
 
-Bio::PanGenome::CommandLine::CreatePanGenome->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::CreatePanGenome->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/extract_proteome_from_gff b/bin/extract_proteome_from_gff
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::ExtractProteomeFromGFF;
+package Bio::Roary::Main::ExtractProteomeFromGFF;
 
 # ABSTRACT: Take in GFF files and output the proteome
 # PODNAME: extract_proteome_from_gff
@@ -14,6 +14,6 @@ Take in GFF files and output the proteome
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::ExtractProteomeFromGff;
+use Bio::Roary::CommandLine::ExtractProteomeFromGff;
 
-Bio::PanGenome::CommandLine::ExtractProteomeFromGff->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::ExtractProteomeFromGff->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/iterative_cdhit b/bin/iterative_cdhit
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::IterativeCdhit;
+package Bio::Roary::Main::IterativeCdhit;
 
 # ABSTRACT: Iteratively run cdhit
 # PODNAME:  iterative_cdhit
@@ -14,6 +14,6 @@ Iteratively run cdhit
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::IterativeCdhit;
+use Bio::Roary::CommandLine::IterativeCdhit;
 
-Bio::PanGenome::CommandLine::IterativeCdhit->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::IterativeCdhit->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/merge_multifasta_alignments b/bin/merge_multifasta_alignments
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::MergeMultipleFastaAlignments;
+package Bio::Roary::Main::MergeMultipleFastaAlignments;
 
 # ABSTRACT: Take in a list of alignment files with equal numbers of sequences and merge them.
 # PODNAME: merge_multifasta_alignments
@@ -14,6 +14,6 @@ Take in a list of alignment files with equal numbers of sequences and merge them
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::MergeMultipleFastaAlignments;
+use Bio::Roary::CommandLine::MergeMultipleFastaAlignments;
 
-Bio::PanGenome::CommandLine::MergeMultipleFastaAlignments->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::MergeMultipleFastaAlignments->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/pan_genome_core_alignment b/bin/pan_genome_core_alignment
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::PanGenomeCoreAlignment;
+package Bio::Roary::Main::RoaryCoreAlignment;
 
 # ABSTRACT: Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.
 # PODNAME: pan_genome_core_alignment
@@ -14,6 +14,6 @@ package Bio::PanGenome::Main::PanGenomeCoreAlignment;
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::PanGenomeCoreAlignment;
+use Bio::Roary::CommandLine::RoaryCoreAlignment;
 
-Bio::PanGenome::CommandLine::PanGenomeCoreAlignment->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::RoaryCoreAlignment->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/pan_genome_post_analysis b/bin/pan_genome_post_analysis
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::PanGenomePostAnalysis;
+package Bio::Roary::Main::RoaryPostAnalysis;
 
 # ABSTRACT: Perform the post analysis on the pan genome
 # PODNAME: pan_genome_post_analysis
@@ -14,6 +14,6 @@ Perform the post analysis on the pan genome
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::PanGenomePostAnalysis;
+use Bio::Roary::CommandLine::RoaryPostAnalysis;
 
-Bio::PanGenome::CommandLine::PanGenomePostAnalysis->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::RoaryPostAnalysis->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/pan_genome_reorder_spreadsheet b/bin/pan_genome_reorder_spreadsheet
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::PanGenomeReorderSpreadsheet;
+package Bio::Roary::Main::RoaryReorderSpreadsheet;
 
 # ABSTRACT: Take in a tree and a spreadsheet and output a reordered spreadsheet
 # PODNAME: pan_genome_reorder_spreadsheet
@@ -14,6 +14,6 @@ Take in a tree and a spreadsheet and output a reordered spreadsheet
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::PanGenomeReorderSpreadsheet;
+use Bio::Roary::CommandLine::RoaryReorderSpreadsheet;
 
-Bio::PanGenome::CommandLine::PanGenomeReorderSpreadsheet->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::RoaryReorderSpreadsheet->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/parallel_all_against_all_blastp b/bin/parallel_all_against_all_blastp
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::ParallelAllAgainstAllBlastp;
+package Bio::Roary::Main::ParallelAllAgainstAllBlastp;
 
 # ABSTRACT: Take in a FASTA file of proteins and blast against itself
 # PODNAME: parallel_all_against_all_blastp
@@ -14,6 +14,6 @@ Take in a FASTA file of proteins and blast against itself
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::ParallelAllAgainstAllBlastp;
+use Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp;
 
-Bio::PanGenome::CommandLine::ParallelAllAgainstAllBlastp->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/protein_muscle_alignment_from_nucleotides b/bin/protein_muscle_alignment_from_nucleotides
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::ProteinMuscleAlignmentFromNucleotides;
+package Bio::Roary::Main::ProteinMuscleAlignmentFromNucleotides;
 
 # ABSTRACT: Take in a multifasta file of nucleotides, convert to proteins and align with muscle
 # PODNAME: protein_muscle_alignment_from_nucleotides
@@ -14,6 +14,6 @@ Take in a multifasta file of nucleotides, convert to proteins and align with mus
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::ProteinMuscleAlignmentFromNucleotides;
+use Bio::Roary::CommandLine::ProteinMuscleAlignmentFromNucleotides;
 
-Bio::PanGenome::CommandLine::ProteinMuscleAlignmentFromNucleotides->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::ProteinMuscleAlignmentFromNucleotides->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/query_pan_genome b/bin/query_pan_genome
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::QueryPanGenome;
+package Bio::Roary::Main::QueryRoary;
 
 # ABSTRACT: Take in a groups file and the protein fasta files and output selected data
 # PODNAME: query_pan_genome
@@ -14,6 +14,6 @@ Take in a groups file and the protein fasta files and output selected data
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::QueryPanGenome;
+use Bio::Roary::CommandLine::QueryRoary;
 
-Bio::PanGenome::CommandLine::QueryPanGenome->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::QueryRoary->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/roary b/bin/roary
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::Roary;
+package Bio::Roary::Main::Roary;
 
 # ABSTRACT: Create a pan genome from a set of proteome FASTA files
 # PODNAME: create_pan_geneome
@@ -14,6 +14,6 @@ Create a pan genome from a set of proteome FASTA files
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::Roary;
+use Bio::Roary::CommandLine::Roary;
 
-Bio::PanGenome::CommandLine::Roary->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::Roary->new(args => \@ARGV, script_name => $0)->run;
diff --git a/bin/transfer_annotation_to_groups b/bin/transfer_annotation_to_groups
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-package Bio::PanGenome::Main::TransferAnnotationToGroups;
+package Bio::Roary::Main::TransferAnnotationToGroups;
 
 # ABSTRACT: Take in a groups file and a set of GFF files and transfer the consensus annotation
 # PODNAME: transfer_annotation_to_groups
@@ -14,6 +14,6 @@ Take in a groups file and a set of GFF files and transfer the consensus annotati
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 #BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
-use Bio::PanGenome::CommandLine::TransferAnnotationToGroups;
+use Bio::Roary::CommandLine::TransferAnnotationToGroups;
 
-Bio::PanGenome::CommandLine::TransferAnnotationToGroups->new(args => \@ARGV, script_name => $0)->run;
+Bio::Roary::CommandLine::TransferAnnotationToGroups->new(args => \@ARGV, script_name => $0)->run;
diff --git a/deployment_process b/deployment_process
@@ -0,0 +1,7 @@
+# Releasing a new version
+
+Update the version number in dist.ini
+Commit all changes.
+Tag with the current version.
+Push all changes, and on github.com submit,accepted pull request
+dzil release
diff --git a/dist.ini b/dist.ini
@@ -1,14 +1,15 @@
-name    = Bio-PanGenome
+name    = Bio-Roary
 version = 2.0.0
 author  = Andrew J. Page <[email protected]>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
 copyright_year   = 2013
+main_module = lib/Bio/Roary.pm
 
 [MetaResources]
 homepage        = http://www.sanger.ac.uk/
-repository.web  = https://github.com/sanger-pathogens/Bio-PanGenome
-repository.url  = https://github.com/sanger-pathogens/Bio-PanGenome.git
+repository.web  = https://github.com/sanger-pathogens/Roary
+repository.url  = https://github.com/sanger-pathogens/Roary.git
 repository.type = git
 
 [RequiresExternal]

diff --git a/lib/Bio/PanGenome/Exceptions.pm b/lib/Bio/PanGenome/Exceptions.pm