Merge branch 'release/v3.7.0'

* Update base image to Ubuntu 20.04

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.7.0
+
+* Update base image to Ubuntu 20.04
+
 ## 3.6.1
 
 * Missing command line arg description in `addVagrentContext.pl`

Dockerfile

@@ -1,14 +1,14 @@
-FROM ubuntu:16.04 as builder
+FROM ubuntu:20.04 as builder
 
 USER root
 
 # ALL tool versions used by opt-build.sh
 # ensure updated in setup.sh too
 ENV VER_BEDTOOLS="2.28.0"
 ENV VER_VCFTOOLS="0.1.16"
-ENV VER_BIODBHTS="2.10"
-ENV VER_HTSLIB="1.9"
-ENV VER_SAMTOOLS="1.9"
+ENV VER_BIODBHTS="3.01"
+ENV VER_HTSLIB="1.10.2"
+ENV VER_SAMTOOLS="1.10"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends \
@@ -49,7 +49,7 @@ RUN bash build/opt-build.sh $OPT
 COPY . .
 RUN bash build/opt-build-local.sh $OPT
 
-FROM ubuntu:16.04
+FROM ubuntu:20.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \

MANIFEST

@@ -1,11 +1,16 @@
+.dockerignore
 .travis.yml
+bin/addVagrentContext.pl
 bin/Admin_CacheFileBuilder.pl
 bin/Admin_EnsemblReferenceFileGenerator.pl
 bin/Admin_EnsemblTranscriptFilter.pl
 bin/Admin_GeneRegionBedDumper.pl
 bin/AnnotateVcf.pl
 bin/cpanm
+build/opt-build-local.sh
+build/opt-build.sh
 CHANGES.md
+Dockerfile
 docs.tar.gz
 lib/Sanger/CGP/Vagrent.pm
 lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm

README.md

@@ -40,11 +40,13 @@ Please be aware that this expects basic C compilation libraries and tools to be
 #### Cutting the release
 1. Update `lib/Sanger/CGP/Vagrent.pm` to the correct version.
 2. Update `CHANGES.md` to show major items.
-3. Run `./prerelease.sh`
-4. Check all tests and coverage reports are acceptable.
-5. Commit the updated docs tree and updated module/version.
-6. Push commits.
-7. Use the GitHub tools to draft a release.
+3. Run `./setup.sh /path/to/local/inst` to create a local installation
+4. Ensure your build enviroment contains Devel::Cover, Template and Pod::Coverage::CountParents. These can be loaded at the Sanger with `module load perl-testlibs`
+5. Run `./prerelease.sh /path/to/local/inst`
+6. Check all tests and coverage reports are acceptable.
+7. Commit the updated docs tree and updated module/version.
+8. Push commits.
+9. Use the GitHub tools to draft a release.
 
 LICENCE
 =======

bin/Admin_CacheFileBuilder.pl

@@ -826,7 +826,7 @@ sub option_builder {
 
 =head1 NAME
 
-Admin_CacheFileBuilder.pl - Generates the Vagrent reference data set from the supplied GFF£/GTF and Fasta files
+Admin_CacheFileBuilder.pl - Generates the Vagrent reference data set from the supplied GFF/GTF and Fasta files
 
 =head1 SYNOPSIS
 

lib/Sanger/CGP/Vagrent.pm

@@ -1,7 +1,7 @@
 package Sanger::CGP::Vagrent;
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT - [email protected]
 #
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.6.1';
+our $VERSION = '3.7.0';
 our @EXPORT = qw($VERSION);
 
 1;

prerelease.sh

@@ -27,6 +27,21 @@ set -eu # exit on first error or undefined value in subtitution
 # get current directory
 INIT_DIR=`pwd`
 
+if [ "$#" -ne "1" ] ; then
+  echo "Please provide the installation path"
+  exit 1
+fi
+
+# Installation path from setup.sh
+INST_PATH=$1
+
+# make sure tools installed can see the install loc of libraries
+set +u
+export PATH=`echo $INST_PATH/bin:$PATH | perl -pe 's/:\$//;'`
+export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'`
+set -u
+
+
 rm -rf blib
 
 # get location of this file

setup.sh

@@ -25,9 +25,9 @@
 # ensure updated in Dockerfile too
 export VER_BEDTOOLS="2.28.0"
 export VER_VCFTOOLS="0.1.16"
-export VER_BIODBHTS="2.10"
-export VER_HTSLIB="1.9"
-export VER_SAMTOOLS="1.9"
+export VER_BIODBHTS="3.01"
+export VER_HTSLIB="1.10.2"
+export VER_SAMTOOLS="1.10"
 
 if [[ ($# -ne 1) ]] ; then
   echo "Please provide an installation path dependencies expected in PATH/PERL5LIB, e.g."