diff --git a/CHANGES.md b/CHANGES.md index 1b15276..190ba88 100644 --- a/CHANGES.md +++ b/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` diff --git a/Dockerfile b/Dockerfile index 7355805..c214c40 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:16.04 as builder +FROM ubuntu:20.04 as builder USER root @@ -6,9 +6,9 @@ USER root # 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="cgphelp@sanger.ac.uk" \ uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \ diff --git a/MANIFEST b/MANIFEST index c7d9ac4..aa811b1 100644 --- a/MANIFEST +++ b/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 diff --git a/README.md b/README.md index 2490a44..6ef4763 100644 --- a/README.md +++ b/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 ======= diff --git a/bin/Admin_CacheFileBuilder.pl b/bin/Admin_CacheFileBuilder.pl index 92a61d3..a4d1eac 100644 --- a/bin/Admin_CacheFileBuilder.pl +++ b/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 diff --git a/docs.tar.gz b/docs.tar.gz index e0ea697..85e41e3 100644 Binary files a/docs.tar.gz and b/docs.tar.gz differ diff --git a/lib/Sanger/CGP/Vagrent.pm b/lib/Sanger/CGP/Vagrent.pm index 8192e3f..cd67a90 100644 --- a/lib/Sanger/CGP/Vagrent.pm +++ b/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 - cgphelp@sanger.ac.uk # @@ -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; diff --git a/prerelease.sh b/prerelease.sh index bd1e009..f38d707 100755 --- a/prerelease.sh +++ b/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 diff --git a/setup.sh b/setup.sh index 336aab8..9cc5425 100755 --- a/setup.sh +++ b/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."