From cbe50d1f3ebd0228520780062acfd82daf8d15c0 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 27 May 2021 14:35:40 +0200
Subject: bioinformatics: Add cgp-cavemanwrapper.

* guix-science/packages/bioinformatics.scm
  (cgp-cavemanwrapper-1.15.2): New variable.
---
 cgp-cavemanwrapper-fix-script.patch | 54 +++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 cgp-cavemanwrapper-fix-script.patch

(limited to 'cgp-cavemanwrapper-fix-script.patch')

diff --git a/cgp-cavemanwrapper-fix-script.patch b/cgp-cavemanwrapper-fix-script.patch
new file mode 100644
index 0000000..75ffd63
--- /dev/null
+++ b/cgp-cavemanwrapper-fix-script.patch
@@ -0,0 +1,54 @@
+diff -crB cgpCaVEManWrapper-1.15.2-orig/bin/caveman_merge_results.pl cgpCaVEManWrapper-1.15.2/bin/caveman_merge_results.pl
+*** cgpCaVEManWrapper-1.15.2-orig/bin/caveman_merge_results.pl	2020-01-17 08:25:27.822179647 +0100
+--- cgpCaVEManWrapper-1.15.2/bin/caveman_merge_results.pl	2020-01-17 08:26:26.735045998 +0100
+***************
+*** 41,47 ****
+  {
+    my $options = setup();
+    merge_vcf($options->{'out'}.'.snps', $options->{'snp_vcf'});
+!   merge_vcf($options->{'out'}.'.subs', $options->{'sub_vcf'});
+    merge_bed($options->{'out'}.'.no_analysis', $options->{'na_bed'});
+  }
+  
+--- 41,47 ----
+  {
+    my $options = setup();
+    merge_vcf($options->{'out'}.'.snps', $options->{'snp_vcf'});
+!   merge_vcf($options->{'out'}.'.muts', $options->{'mut_vcf'});
+    merge_bed($options->{'out'}.'.no_analysis', $options->{'na_bed'});
+  }
+  
+***************
+*** 66,72 ****
+  	my ($path_prefix, $bed_files) = @_;
+    my $new_bed = $path_prefix.'.bed';
+    my $new_tmp_bed = $path_prefix.'.tmp.bed';
+!   system(qq{grep '^#' $bed_files->[0] > $new_tmp_bed});
+    system(qq{cat @{$bed_files} | grep -v '^#' | sort -k1,1 -k2,2n >> $new_tmp_bed});
+  
+  	#Now merge the bed file with bedtools merge so we have a much smaller output file.
+--- 66,72 ----
+  	my ($path_prefix, $bed_files) = @_;
+    my $new_bed = $path_prefix.'.bed';
+    my $new_tmp_bed = $path_prefix.'.tmp.bed';
+! #  system(qq{grep '^#' $bed_files->[0] > $new_tmp_bed});
+    system(qq{cat @{$bed_files} | grep -v '^#' | sort -k1,1 -k2,2n >> $new_tmp_bed});
+  
+  	#Now merge the bed file with bedtools merge so we have a much smaller output file.
+***************
+*** 103,109 ****
+      if($file =~ m/\.snps\.vcf$/) {
+        push @{$opts{'snp_vcf'}}, $file;
+      }elsif($file =~ m/\.muts\.vcf$/){
+!     	push @{$opts{'snp_vcf'}}, $file;
+      }
+      elsif($file =~ m/\.no_analysis\.bed$/) {
+        push @{$opts{'na_bed'}}, $file;
+--- 103,109 ----
+      if($file =~ m/\.snps\.vcf$/) {
+        push @{$opts{'snp_vcf'}}, $file;
+      }elsif($file =~ m/\.muts\.vcf$/){
+!     	push @{$opts{'mut_vcf'}}, $file;
+      }
+      elsif($file =~ m/\.no_analysis\.bed$/) {
+        push @{$opts{'na_bed'}}, $file;
-- 
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