[med-svn] [roary] 04/07: add patches for manpage generation and script rename

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository roary.

commit 3227e01b06e44138242e7ff10ea1ed353b7306a1
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sun Dec 20 13:40:29 2015 +0000

    add patches for manpage generation and script rename
---
 debian/patches/add_abstract.patch    | 40 ++++++++++++++++++++++++++++++
 debian/patches/rename_R_script.patch | 11 +++++++++
 debian/patches/series                |  3 +++
 debian/patches/spelling.patch        | 48 ++++++++++++++++++++++++++++++++++++
 4 files changed, 102 insertions(+)

diff --git a/debian/patches/add_abstract.patch b/debian/patches/add_abstract.patch
new file mode 100644
index 0000000..02a6afa
--- /dev/null
+++ b/debian/patches/add_abstract.patch
@@ -0,0 +1,40 @@
+--- a/lib/Bio/Roary/SplitGroups.pm
++++ b/lib/Bio/Roary/SplitGroups.pm
+@@ -1,6 +1,6 @@
+ package Bio::Roary::SplitGroups;
+ 
+-# ABSTRACT: 
++# ABSTRACT: split groups
+ 
+ =head1 SYNOPSIS
+ 
+@@ -52,7 +52,7 @@
+ 
+ sub _build__analyse_groups_obj {
+ 	my ( $self ) = @_;
+-	
++
+ 	return Bio::Roary::AnalyseGroups->new(
+ 		fasta_files     => $self->fasta_files,
+ 		groups_filename => $self->groupfile
+@@ -85,9 +85,9 @@
+   {
+ 	my ( $filename, $directories, $suffix ) = fileparse( $fasta_file, qr/\.[^.]*/ );
+   	system('grep \> '.$fasta_file.'| sed  \'s/>//\' >'.$self->_gene_files_temp_dir_obj."/".$filename.$suffix ) ;
+-	
++
+ 	my @genes = read_lines($self->_gene_files_temp_dir_obj."/".$filename.$suffix );
+-	
++
+ 	for(my $i =0; $i< @genes; $i++)
+ 	{
+ 		for(my $offset = 1; $offset <= $self->_neighbourhood_size; $offset++)
+@@ -111,7 +111,7 @@
+ 
+ 	# iteratively
+ 	for my $x ( 0..($self->iterations - 1) ){
+-		my ( $in_groups, $out_groups ) = $self->_get_files_for_iteration( $x ); 
++		my ( $in_groups, $out_groups ) = $self->_get_files_for_iteration( $x );
+ 
+ 		# read in groups, check paralogs and split
+ 		my @newgroups;
diff --git a/debian/patches/rename_R_script.patch b/debian/patches/rename_R_script.patch
new file mode 100644
index 0000000..4718f63
--- /dev/null
+++ b/debian/patches/rename_R_script.patch
@@ -0,0 +1,11 @@
+--- a/lib/Bio/Roary/PostAnalysis.pm
++++ b/lib/Bio/Roary/PostAnalysis.pm
+@@ -125,7 +125,7 @@
+     $self->logger->info("Creating tab files for R");
+     $self->_number_of_groups_obj->create_output_files;
+ 
+-    system("create_pan_genome_plots.R") unless ( $self->dont_create_rplots == 1 );
++    system("create_pan_genome_plots") unless ( $self->dont_create_rplots == 1 );
+ 
+     $self->logger->info("Create EMBL files");
+     $self->_create_embl_files;
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..51f63b5
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+rename_R_script.patch
+add_abstract.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..4ce6e6d
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,48 @@
+--- a/bin/pan_genome_assembly_statistics
++++ b/bin/pan_genome_assembly_statistics
+@@ -2,12 +2,12 @@
+ 
+ package Bio::Roary::Main::AssemblyStatistics;
+ 
+-# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
++# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
+ # PODNAME: pan_genome_assembly_statistics
+ 
+ =head1 SYNOPSIS
+ 
+-Given a spreadsheet of gene presence and absense calculate some statistics
++Given a spreadsheet of gene presence and absence calculate some statistics
+ 
+ =cut
+ 
+--- a/lib/Bio/Roary/AssemblyStatistics.pm
++++ b/lib/Bio/Roary/AssemblyStatistics.pm
+@@ -1,10 +1,10 @@
+ package Bio::Roary::AssemblyStatistics;
+ 
+-# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
++# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
+ 
+ =head1 SYNOPSIS
+ 
+-Given a spreadsheet of gene presence and absense calculate some statistics
++Given a spreadsheet of gene presence and absence calculate some statistics
+ 
+ =cut
+ 
+--- a/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
++++ b/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
+@@ -1,11 +1,11 @@
+ undef $VERSION;
+ package Bio::Roary::CommandLine::AssemblyStatistics;
+ 
+-# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
++# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
+ 
+ =head1 SYNOPSIS
+ 
+-Given a spreadsheet of gene presence and absense calculate some statistics
++Given a spreadsheet of gene presence and absence calculate some statistics
+ 
+ =cut
+ 

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