Merge tag 'v6.3.4' into dev

Change bedtools due to errors in subsets of data, fix version of gam due to recent lib (R) change

Author: keiranmraine

CHANGES.md

@@ -1,5 +1,10 @@
 # Changes
 
+## v6.3.4
+
+* Bedtools 2.28.0 binary caused stack collision.
+* Fix R package `gam` to 1.16.1 due to change in behaviour of 1.20 (5th July 2020).
+
 ## v6.3.3
 
 * Singularity specific execution issue corrected

Dockerfile

@@ -3,7 +3,7 @@ FROM  quay.io/wtsicgp/pcap-core:5.0.5 as builder
 USER  root
 
 # ALL tool versions used by opt-build.sh
-ENV VER_BEDTOOLS="2.28.0"
+ENV VER_BEDTOOLS="2.29.2"
 ENV VER_VCFTOOLS="0.1.16"
 ENV VER_BLAT="35"
 ENV VER_CGPVCF="v2.2.1"
@@ -69,7 +69,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="v6.3.3" \
+      version="v6.3.4" \
       description="BRASS docker"
 
 RUN apt-get -yq update \

Rsupport/libInstall.R

@@ -18,7 +18,7 @@ library(devtools)
 options(download.file.method = "auto")
 
 ipak(c("data.table"))
-ipak(c("gam"))
+install_github("cran/gam", ref="1.16.1")
 
 if ( version$major == 3 && version$minor < 2 ) {
   install.packages("VGAM_1.0-3.tar.gz", type="source", lib=instLib, lib.loc=instLib)

build/opt-build.sh

@@ -78,7 +78,7 @@ fi
 
 ## bedtools
 if [ ! -e $SETUP_DIR/bedtools.success ]; then
-  curl -sSL --retry 10 -o $INST_PATH/bin/bedtools https://github.com/arq5x/bedtools2/releases/download/v${VER_BEDTOOLS}/bedtools
+  curl -sSL --retry 10 -o $INST_PATH/bin/bedtools https://github.com/arq5x/bedtools2/releases/download/v${VER_BEDTOOLS}/bedtools.static.binary
   chmod +x $INST_PATH/bin/bedtools
   chmod -w $INST_PATH/bin/bedtools
   touch $SETUP_DIR/bedtools.success

perl/bin/brassI_prep_bam.pl

@@ -76,8 +76,10 @@ sub run {
     my ($rname,$mapq,$rnext,$tlen,$seq) = (split /\t/, $r1)[2,4,6,8,9];
     next if($mapq < $MIN_MAPQ);
     next if(($rnext eq '=' || $rname eq $rnext) && abs $tlen < (length $seq) * 2);
-    next unless(first { $rname eq $_ } @good_seqs);
-    next unless(first { $rnext eq $_ } @good_seqs);
+    if(defined $options->{include}) {
+      next unless(first { $rname eq $_ } @good_seqs);
+      next unless(first { $rnext eq $_ } @good_seqs);
+    }
     my $mapq2 = (split /\t/, $r2)[4];
     next if($mapq2 < $MIN_MAPQ);
 

perl/lib/Bio/Brass.pm

@@ -46,7 +46,7 @@ our @EXPORT = qw(find_breakpoints find_dusty_vertices
 		 is_dusty get_isolated_bp_alignment get_isolated_bp_surrounding_region
 		 $VERSION);
 
-our $VERSION = '6.3.3';
+our $VERSION = '6.3.4';
 
 =head1 NAME
 

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

@@ -128,7 +128,7 @@ sub input {
     $helper_threads = 6 if($helper_threads > 6);
 
     my $command = _which('samtools');
-    $command .= ' view -F 3854 -q 6 -u '.$input;
+    $command .= ' view -F 3854 -q 6 -u '.$input.' '.join(' ', valid_seqs($options));
     $command .= ' | ';
     $command .= _which('bedtools');
     $command .= sprintf $BED_INTERSECT_V, 'stdin', $options->{'depth'};
@@ -139,7 +139,6 @@ sub input {
     $command .= "$^X ";
     $command .= _which('brassI_prep_bam.pl');
     $command .= sprintf $PREP_BAM, $input.'.bas', $rg_prefix;
-    $command .= " -i ".join(',', valid_seqs($options));
     $command .= ' | ';
     $command .= _which('bamsort');
     $command .= sprintf $BAMSORT, $tmp, $index, $outbam, $outbam, $outbam, $helper_threads, $helper_threads;

setup.sh

@@ -35,7 +35,7 @@
 SOURCE_BLAT="https://hgwdev.gi.ucsc.edu/~kent/src/blatSrc35.zip"
 
 # if issues found downgrade to 2.23.0 but can't find any use of bedtools coverage
-SOURCE_BEDTOOLS="https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz"
+SOURCE_BEDTOOLS="https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools-2.29.2.tar.gz"
 
 get_distro () {
   EXT=""