Updated all version info for Release v0.16.0

RELEASE_NOTES.txt

@@ -1,4 +1,4 @@
-RELEASE NOTES FOR Bismark v0.15.1_dev (18 04 2016)
+RELEASE NOTES FOR Bismark v0.16.0 (20 04 2016)
 ----------------------------------------------
 
 Bismark

bam2nuc

@@ -31,7 +31,7 @@ my %freqs;   # keeping a record of which chromosomes have been processed
 my %genomic_freqs;
 my %processed;
 
-my $bam2nuc_version = 'v0.15.1';
+my $bam2nuc_version = 'v0.16.0';
 
 my ($output_dir,$genome_folder,$parent_dir,$samtools_path) = process_commandline();
 

bismark

@@ -25,7 +25,7 @@ use lib "$Bin/../lib";
 
 
 my $parent_dir = getcwd;
-my $bismark_version = 'v0.15.1_dev';
+my $bismark_version = 'v0.16.0';
 my $command_line = join (" ",@ARGV);
 
 

bismark2bedGraph

@@ -21,7 +21,7 @@ use Carp;
 ## You should have received a copy of the GNU General Public License
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-my $bismark2bedGraph_version = 'v0.15.1';
+my $bismark2bedGraph_version = 'v0.16.0';
 
 my @bedfiles;
 my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total

bismark2report

@@ -20,7 +20,7 @@ use lib "$Bin/../lib";
 ## You should have received a copy of the GNU General Public License
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-my $bismark2report_version = 'v0.15.1';
+my $bismark2report_version = 'v0.16.0';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

bismark2summary

@@ -17,7 +17,7 @@ use strict;
 
 ## You should have received a copy of the GNU General Public License
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
-my $bismark_version = '0.15.2';
+my $bismark_version = '0.16.0';
 
 # Last modified 03 03 2016
 

bismark_genome_preparation

@@ -34,7 +34,7 @@ my $single_fasta;
 my $bowtie2;
 my $bowtie1;
 
-my $bismark_version = 'v0.15.0';
+my $bismark_version = 'v0.16.0';
 
 GetOptions ('verbose' => \$verbose,
 	    'help' => \$help,

bismark_methylation_extractor

@@ -29,7 +29,7 @@ my $parent_dir = getcwd();
 
 my %fhs;
 
-my $version = 'v0.15.0';
+my $version = 'v0.16.0';
 my ($ignore,$genomic_fasta,$single,$paired,$full,$report,$no_overlap,$merge_non_CpG,$vanilla,$output_dir,$no_header,$bedGraph,$remove,$coverage_threshold,$counts,$cytosine_report,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$sort_size,$samtools_path,$gzip,$ignore_r2,$mbias_off,$mbias_only,$gazillion,$ample_mem,$ignore_3prime,$ignore_3prime_r2,$multicore) = process_commandline();
 
 

copy_bismark_files_for_release.pl

@@ -0,0 +1,45 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+use File::Copy "cp";
+
+my $dir = shift@ARGV;
+
+die "Please provide a directory to copy files to!\n\n" unless ($dir);
+
+unless (-d $dir){
+  warn "Specified directory '$dir' doesn't exist. Creating it for you...\n\n";
+  mkdir $dir or die "Failed to create directory: $!\n\n";
+}
+
+my @files = ('RELEASE_NOTES.txt','bismark','bismark_genome_preparation','bismark_methylation_extractor','bismark2bedGraph','bismark2report','coverage2cytosine','license.txt','Bismark_User_Guide.pdf','RRBS_Guide.pdf','deduplicate_bismark','bismark_sitrep.tpl','bam2nuc','bismark2summary');
+
+foreach my $file (@files){
+  copy_and_warn($file);
+}
+
+sub copy_and_warn{
+  my $file = shift;
+  warn "Now copying '$file' to $dir\n";
+  cp($file,"$dir/") or die "Copy failed: $!";
+
+}
+
+@files = ('bismark','bismark_genome_preparation','bismark_methylation_extractor','bismark2bedGraph','bismark2report','coverage2cytosine','deduplicate_bismark','bam2nuc','bismark2summary');
+
+foreach my $file (@files){
+  set_permissions($file);
+}
+
+sub set_permissions{
+  my $file = shift;
+  warn "Setting permissions for ${dir}/$file\n";
+  chmod 0755, "${dir}/$file";
+}
+
+
+### Taring up the folder
+$dir =~ s/\/$//;
+warn "Tar command:\ntar czvf ${dir}.tar.gz $dir\n\n";
+sleep(3);
+system ("tar czvf ${dir}.tar.gz $dir/");

coverage2cytosine

@@ -23,7 +23,7 @@ use Carp;
 
 my %chromosomes; # storing sequence information of all chromosomes/scaffolds
 my %processed;   # keeping a record of which chromosomes have been processed
-my $coverage2cytosine_version = 'v0.15.1_dev';
+my $coverage2cytosine_version = 'v0.16.0';
 
 my ($output_dir,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$parent_dir,$coverage_infile,$cytosine_out,$merge_CpGs,$gc_context,$gzip,$tetra) = process_commandline();
 

deduplicate_bismark

@@ -30,7 +30,7 @@ use Getopt::Long;
 ### print "--representative\twill browse through all sequences and print out the sequence with the most representative (as in most frequent) methylation call for any given position. Note that this is very likely the most highly amplified PCR product for a given sequence\n\n";
 
 
-my $dedup_version = 'v0.14.6';
+my $dedup_version = 'v0.16.0';
 
 
 my $help;