Merge branch 'hotfix/4.4.1'

CHANGES.md

@@ -1,5 +1,9 @@
 # Changes
 
+## 4.4.1
+
+* Update base image for performance from htslib 1.11.
+
 ## 4.4.0
 
 * Added ascatCounts to produce counts files

Dockerfile

@@ -1,11 +1,11 @@
-FROM quay.io/wtsicgp/pcap-core:5.2.1 as builder
+FROM quay.io/wtsicgp/pcap-core:5.4.2 as builder
 
 USER root
 
 # ALL tool versions used by opt-build.sh
 ENV VER_CGPVCF="v2.2.1"
 ENV VER_VCFTOOLS="0.1.16"
-ENV VER_ALLELECOUNT="4.1.0"
+ENV VER_ALLELECOUNT="v4.2.1"
 
 RUN apt-get -yq update
 
@@ -15,7 +15,7 @@ RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`-cran40/
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 RUN apt-get -yq update
 
-ENV DEBIAN_FRONTEND "noninteractive" 
+ENV DEBIAN_FRONTEND "noninteractive"
 # no benefit of combined in builder stage
 RUN apt-get install -yq --no-install-recommends locales
 RUN apt-get install -yq --no-install-recommends g++
@@ -80,14 +80,13 @@ FROM ubuntu:20.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="4.3.4" \
       description="Ascat NGS docker"
 
 RUN apt-get -yq update \
 && apt-get install -qy --no-install-recommends lsb-release \
 gnupg
 
-ENV DEBIAN_FRONTEND "noninteractive" 
+ENV DEBIAN_FRONTEND "noninteractive"
 RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`-cran40/" >> /etc/apt/sources.list \
 && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
 && apt-get -yq update \

README.md

@@ -102,7 +102,7 @@ Please see the [wiki][ascatngs-wiki] for how to obtain/generate the
 ## LICENCE
 
 ```
-Copyright (c) 2014-2019 Genome Research Ltd.
+Copyright (c) 2014-2020 Genome Research Ltd.
 
 Author: CASM/Cancer IT <[email protected]>
 

build/opt-build.sh

@@ -49,48 +49,6 @@ export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/
 export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'`
 set -u
 
-# ## INSTALL CPANMINUS
-# set -eux
-# curl -sSL https://cpanmin.us/ > $SETUP_DIR/cpanm
-# perl $SETUP_DIR/cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH App::cpanminus
-# rm -f $SETUP_DIR/cpanm
-
-# ## HTSLIB (tar.bz2)
-# if [ ! -e $SETUP_DIR/htslib.success ]; then
-#   rm -rf htslib
-#   mkdir -p htslib
-#   curl -sSL --retry 10 https://github.com/samtools/htslib/releases/download/${VER_HTSLIB}/htslib-${VER_HTSLIB}.tar.bz2 > distro.tar.bz2
-#   tar --strip-components 1 -C htslib -jxf distro.tar.bz2
-#   cd htslib
-#   ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
-#   make clean
-#   make -j$CPU
-#   make install
-#   cd $SETUP_DIR
-#   rm -rf distro.*
-#   touch $SETUP_DIR/htslib.success
-# fi
-
-# ## Bio::DB::HTS (tar.gz)
-# if [ ! -e $SETUP_DIR/Bio-DB-HTS.success ]; then
-#   ## add perl deps
-#   cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH Module::Build
-#   cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH XML::Parser
-#   cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH Bio::Root::Version
-
-#   curl -sSL --retry 10 https://github.com/Ensembl/Bio-DB-HTS/archive/${VER_BIODBHTS}.tar.gz > distro.tar.gz
-#   rm -rf distro/*
-#   tar --strip-components 1 -C distro -zxf distro.tar.gz
-#   cd distro
-#   perl Build.PL --install_base=$INST_PATH --htslib=$INST_PATH
-#   ./Build
-#   ./Build test
-#   ./Build install
-#   cd $SETUP_DIR
-#   rm -rf distro.* distro/*
-#   touch $SETUP_DIR/Bio-DB-HTS.success
-# fi
-
 ## vcftools
 if [ ! -e $SETUP_DIR/vcftools.success ]; then
   curl -sSL --retry 10 https://github.com/vcftools/vcftools/releases/download/v${VER_VCFTOOLS}/vcftools-${VER_VCFTOOLS}.tar.gz > distro.tar.gz
@@ -126,7 +84,8 @@ if [ ! -e $SETUP_DIR/alleleCount.success ]; then
   cd distro
   if [ ! -e $SETUP_DIR/alleleCount_c.success ]; then
     make -C c clean
-    make -C c -j$CPU prefix=$INST_PATH HTSLIB=$INST_PATH/lib
+    export prefix=$INST_PATH
+    make -C c -j$CPU
     cp c/bin/alleleCounter $INST_PATH/bin/.
     touch $SETUP_DIR/alleleCount_c.success
   fi

perl/Makefile.PL

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/ascat.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -68,7 +68,7 @@ BEGIN
   if ( $options->{'counts_input'} == 1) {
     my $ascat_out = File::Spec->catdir(abs_path($options->{'tmp'}),'ascat');
     make_path($ascat_out) unless(-e $ascat_out);
-    $threads->run(2, 'deploy_counts', $options);    
+    $threads->run(2, 'deploy_counts', $options);
   }
   Sanger::CGP::Ascat::Implement::ascat($options) if(!exists $options->{'process'} || $options->{'process'} eq 'ascat');
   if(!exists $options->{'process'} || $options->{'process'} eq 'finalise') {

perl/bin/ascatCnToVCF.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -50,14 +50,14 @@ BEGIN
 
 {
   my $opts = setup();
-  
+
   my $contigs;
   my $mt_samples;
   my $wt_samples;
 
   #If tumour and sample name are provided dont require BAM or ref files
   #and must build sample and ref object here
-  if ( defined $opts->{'tn'} and defined $opts->{'nn'} ) { 
+  if ( defined $opts->{'tn'} and defined $opts->{'nn'} ) {
     $mt_samples->{ $opts->{'tn'} } = new Sanger::CGP::Vcf::Sample(
         -name => $opts->{'tn'} ,
         -study => undef,
@@ -239,7 +239,7 @@ sub setup{
     pod2usage(-message  => "\nERROR: When using sample name arguments ref. species must be specified (-rs)\n", -verbose => 1,  -output => \*STDERR) if( !( defined $opts{'rs'} && defined $opts{'rs'}) );
     pod2usage(-message  => "\nERROR: When using sample name arguments sequencing platform must be specified (-wsp & -msp)\n", -verbose => 1,  -output => \*STDERR) if( !( defined $opts{'wsp'} && defined $opts{'wsp'})  and !( defined $opts{'msp'} && defined $opts{'msp'}) );
     return \%opts;
-  } 
+  }
 
   PCAP::Cli::file_for_reading('sbm', $opts{'sbm'});
   PCAP::Cli::file_for_reading('sbw', $opts{'sbw'});
@@ -279,7 +279,7 @@ =head1 SYNOPSIS
       -sample-accession-source-norm    -wsc  Normal sample accession source.
       -seq-platform-norm               -wsp  Normal sequencing platform [BAM HEADER].
 
- 
+
     Other:
      -tumour_name    -tn  Tumour sample name. For processing count file results
      -normal_name    -nn  Normal sample name. For processing count file results

perl/bin/ascatCounts.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -50,7 +50,7 @@ BEGIN
   $options->{'tumour'} = $options->{'bam'}; #map input file to tumour
   $options->{'tumour_name'} = (PCAP::Bam::sample_name($options->{'bam'}))[0];
   my $threads = PCAP::Threaded->new($options->{'threads'});
-  
+
   # register any process that can run in parallel here
   $threads->add_function('allele_count', \&Sanger::CGP::Ascat::Implement::allele_count);
 
@@ -149,7 +149,7 @@ sub setup {
   make_path($logs) unless(-d $logs);
 
   $opts{'tmp'} = $tmpdir;
-  
+
   return \%opts;
 }
 

perl/bin/ascatFailedCnCsv.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/ascatToBigWig.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/utilities/ascatFaiChunk.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/utilities/ascatSnpPanelFromVcfs.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/utilities/ascatSnpPanelGcCorrections.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/utilities/ascatSnpPanelGenerator.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/bin/utilities/ascatSnpPanelMerge.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/lib/Sanger/CGP/Ascat.pm

@@ -1,5 +1,5 @@
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -26,12 +26,12 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '4.4.0';
+our $VERSION = '4.4.1';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
 '##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/lib/Sanger/CGP/Ascat/Implement.pm

@@ -1,5 +1,5 @@
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -530,7 +530,7 @@ sub deploy_counts {
   if ($index_in == 2 ){
     push @commands, sprintf 'zcat %s > %s',$options->{'normal'}, $normcount;
   }
-  PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), \@commands, 0); 
+  PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), \@commands, 0);
 }
 
 1;

perl/share/ascat/runASCAT.R

@@ -1,5 +1,5 @@
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: Peter Van Loo <[email protected]>
 #

perl/t/1_pm_compile.t

@@ -1,5 +1,5 @@
 ########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/t/2_pl_compile.t

@@ -1,5 +1,5 @@
 ########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

perl/t/CN_to_VCF.t

@@ -1,5 +1,5 @@
 ##########LICENCE##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

prerelease.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #

setup.sh

@@ -36,7 +36,7 @@
 # need to keep in sync with Dockerfile
 export VER_CGPVCF="v2.2.1"
 export VER_VCFTOOLS="0.1.16"
-export VER_ALLELECOUNT="4.1.0"
+export VER_ALLELECOUNT="v4.2.1"
 
 get_file () {
 # output, source