From 65214d14b6b10c3465ca35bfb1ed9066bc79025d Mon Sep 17 00:00:00 2001 From: FelixKrueger Date: Wed, 20 Apr 2016 13:51:27 +0100 Subject: [PATCH] Updated all version info for Release v0.16.0 --- RELEASE_NOTES.txt | 2 +- bam2nuc | 2 +- bismark | 2 +- bismark2bedGraph | 2 +- bismark2report | 2 +- bismark2summary | 2 +- bismark_genome_preparation | 2 +- bismark_methylation_extractor | 2 +- copy_bismark_files_for_release.pl | 45 +++++++++++++++++++++++++++++++ coverage2cytosine | 2 +- deduplicate_bismark | 2 +- 11 files changed, 55 insertions(+), 10 deletions(-) create mode 100755 copy_bismark_files_for_release.pl diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt index 2064624..6d94969 100644 --- a/RELEASE_NOTES.txt +++ b/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 diff --git a/bam2nuc b/bam2nuc index e7fc135..d3f310f 100755 --- a/bam2nuc +++ b/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,$samtools_path) = process_commandline(); diff --git a/bismark b/bismark index 388e84b..69e4bbd 100755 --- a/bismark +++ b/bismark @@ -25,7 +25,7 @@ use lib "$Bin/../lib"; my $parent_dir = getcwd; -my $bismark_version = 'v0.15.1_dev'; +my $bismark_version = 'v0.16.0'; my $command_line = join (" ",@ARGV); diff --git a/bismark2bedGraph b/bismark2bedGraph index 52f0b87..d621d26 100755 --- a/bismark2bedGraph +++ b/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 . -my $bismark2bedGraph_version = 'v0.15.1'; +my $bismark2bedGraph_version = 'v0.16.0'; my @bedfiles; my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total diff --git a/bismark2report b/bismark2report index 0ce7635..35ea4a9 100755 --- a/bismark2report +++ b/bismark2report @@ -20,7 +20,7 @@ use lib "$Bin/../lib"; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -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(); diff --git a/bismark2summary b/bismark2summary index fa13ccc..c8cbc87 100755 --- a/bismark2summary +++ b/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 . -my $bismark_version = '0.15.2'; +my $bismark_version = '0.16.0'; # Last modified 03 03 2016 diff --git a/bismark_genome_preparation b/bismark_genome_preparation index 008f3ae..6c4c584 100755 --- a/bismark_genome_preparation +++ b/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, diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor index c309fdd..65554b6 100755 --- a/bismark_methylation_extractor +++ b/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(); diff --git a/copy_bismark_files_for_release.pl b/copy_bismark_files_for_release.pl new file mode 100755 index 0000000..a6e74a3 --- /dev/null +++ b/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/"); diff --git a/coverage2cytosine b/coverage2cytosine index 6104932..c7495df 100755 --- a/coverage2cytosine +++ b/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(); diff --git a/deduplicate_bismark b/deduplicate_bismark index c938da5..13abb19 100755 --- a/deduplicate_bismark +++ b/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;