Merge branch 'hotfix/v3.6.1'

cancerit · May 6, 2020 · 0348d46 · 0348d46
2 parents ae48e42 + 9dd3b77
commit 0348d46
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Showing 4 changed files with 11 additions and 6 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.6.1
+
+* Missing command line arg description in `addVagrentContext.pl`
+
 ## 3.6.0
 
 * Adds `addVagrentContext.pl` to replace unsupported internal code.

diff --git a/Dockerfile b/Dockerfile
@@ -53,7 +53,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="3.6.0" \
+      version="3.6.1" \
       description="VAGrENT genome annotation docker"
 
 RUN apt-get -yq update

diff --git a/bin/addVagrentContext.pl b/bin/addVagrentContext.pl
@@ -11,10 +11,11 @@
 
 if(@ARGV < 4) {
   print STDERR "USAGE: genome.fa vagrent.cache.gz bases_context loci_in.tab [pad_gene]\n\n";
-  print STDERR "  genome.fa     = reference genome fasta with fai index.\n";
-  print STDERR "  bases_context = Number of surrounding context bases (N +/-).\n";
-  print STDERR "  loci_in.tab   = tab delimited file beginning: 'chr\\tpos...\\n'.\n";
-  print STDERR "  pad_gene      = 1 indicates that coordinates for gene overlap are padded with 'bases_context'\n";
+  print STDERR "  genome.fa        = reference genome fasta with fai index.\n";
+  print STDERR "  vagrent.cache.gz = VAGrENT cache file.\n";
+  print STDERR "  bases_context    = Number of surrounding context bases (N +/-).\n";
+  print STDERR "  loci_in.tab      = tab delimited file beginning: 'chr\\tpos...\\n'.\n";
+  print STDERR "  pad_gene         = 1 indicates that coordinates for gene overlap are padded with 'bases_context'\n";
   print STDERR "\nIf first line of input prefixed # understood to be header and new headings added\n";
   print STDERR "Ouput is original line with '\\tWT\\tCONTEXT\\tGENE\\tSTRAND' appended\n";
   exit 1;

diff --git a/lib/Sanger/CGP/Vagrent.pm b/lib/Sanger/CGP/Vagrent.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.6.0';
+our $VERSION = '3.6.1';
 our @EXPORT = qw($VERSION);
 
 1;