Merge branch 'release/1.3.0'

CHANGES.md

@@ -1,5 +1,13 @@
 # CHANGES
 
+## 1.3.0
+
+* Update to htslib 1.10.2
+  * Required for PCAP-core to update to samtools 1.10 for new features
+* Update `setup.sh` to exec `build/*` scripts to reduce chance of divergence
+* Update Docker image to Ubuntu Focal (20.04) base.
+* Fix #33 (typo)
+
 ## 1.2.0
 
 Add bam2bw -S/--scale-log10 to enable simple RPKM rescaling.

Dockerfile

@@ -1,8 +1,10 @@
-FROM  ubuntu:16.04 as builder
+FROM  ubuntu:20.04 as builder
 
 USER  root
 
-ARG VER_HTSLIB="1.9"
+# ALL tool versions used by opt-build.sh
+# need to keep in sync with setup.sh
+ARG VER_HTSLIB="1.10.2"
 ARG VER_LIBBW="0.4.2"
 
 ENV OPT /opt/wtsi-cgp
@@ -11,24 +13,23 @@ ENV LD_LIBRARY_PATH $OPT/lib
 ENV LC_ALL C
 
 RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends\
-  build-essential\
-  apt-transport-https\
-  curl\
-  ca-certificates\
-  make\
-  bzip2\
-  gcc\
-  libtasn1-dev\
-  libgnutls-dev\
-  nettle-dev\
-  libgmp-dev\
-  libp11-kit-dev\
-  zlib1g-dev\
-  libbz2-dev\
-  liblzma-dev\
-  libcurl4-gnutls-dev\
-  libncurses5-dev
+RUN apt-get install -yq --no-install-recommends build-essential
+RUN apt-get install -yq --no-install-recommends apt-transport-https
+RUN apt-get install -yq --no-install-recommends curl
+RUN apt-get install -yq --no-install-recommends ca-certificates
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends bzip2
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends libtasn1-dev
+RUN apt-get install -yq --no-install-recommends nettle-dev
+RUN apt-get install -yq --no-install-recommends libgmp-dev
+RUN apt-get install -yq --no-install-recommends libp11-kit-dev
+RUN apt-get install -yq --no-install-recommends zlib1g-dev
+RUN apt-get install -yq --no-install-recommends libbz2-dev
+RUN apt-get install -yq --no-install-recommends liblzma-dev
+RUN apt-get install -yq --no-install-recommends libcurl4-gnutls-dev
+RUN apt-get install -yq --no-install-recommends libncurses5-dev
+RUN apt-get install -yq --no-install-recommends libgnutls28-dev
 
 RUN mkdir -p $OPT/bin
 
@@ -40,11 +41,11 @@ 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 Sanger Institute" \
-      version="1.2.0" \
+      version="1.3.0" \
       description="cgpBigWig"
 
 ENV OPT /opt/wtsi-cgp
@@ -61,6 +62,7 @@ bzip2 \
 zlib1g \
 liblzma5 \
 libncurses5 \
+libcurl3-gnutls \
 unattended-upgrades && \
 unattended-upgrade -d -v && \
 apt-get remove -yq unattended-upgrades && \

VERSION.txt

@@ -1 +1 @@
-1.1.0
+1.3.0

c/bam2bwbases.c

@@ -64,7 +64,7 @@ void print_usage (int exit_code){
   printf("-f  --filter-include [int]                        SAM flags to include. [default: %d]\n",filterinc);
   printf("                                                  N.B. if properly paired reads are filtered for inclusion bam2bw will assume paired-end data\n");
   printf("                                                  and exclude any proper-pair flagged reads not in F/R orientation.");
-	printf("-o  --outfile [file]                              Path to the output .bw file produced. Per base results wiillbe output as four bw files [ACGT].outputname.bw [default:'%s']\n\n",out_file);
+	printf("-o  --outfile [file]                              Path to the output .bw file produced. Per base results will be output as four bw files [ACGT].outputname.bw [default:'%s']\n\n",out_file);
 	printf("Optional: \n");
 	printf("-c  --region [file]                               A samtools style region (contig:start-stop) or a bed file of regions over which to produce the bigwig file\n");
 	printf("-r  --reference [file]                            Path to reference genome.fa file (required for cram if ref_path cannot be resolved)\n");

setup.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 ########## LICENSE ##########
-# Copyright (c) 2016 Genome Research Ltd.
+# Copyright (c) 2016-2020 Genome Research Ltd.
 #
 # Author: Cancer Genome Project [email protected]
 #
@@ -32,147 +32,41 @@
 #
 ###########################
 
-# for bamstats
-SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2"
-#libBigWig - bigwig access library
-SOURCE_LIB_BW="https://github.com/dpryan79/libBigWig/archive/0.4.2.tar.gz"
-
-get_distro () {
-  EXT=""
-  if [[ $2 == *.tar.bz2* ]] ; then
-    EXT="tar.bz2"
-  elif [[ $2 == *.zip* ]] ; then
-    EXT="zip"
-  elif [[ $2 == *.tar.gz* ]] ; then
-    EXT="tar.gz"
-  else
-    echo "I don't understand the file type for $1"
-    exit 1
-  fi
-  if hash curl 2>/dev/null; then
-    curl -sS -o $1.$EXT -L $2
-  else
-    wget -nv -O $1.$EXT $2
-  fi
-}
-
-get_file () {
-# output, source
-  if hash curl 2>/dev/null; then
-    curl -sS -o $1 -L $2
-  else
-    wget -nv -O $1 $2
-  fi
-}
-
-if [ "$#" -ne "1" ] ; then
-  echo "Please provide an installation path  such as /opt/ICGC"
-  exit 0
-fi
-
-CPU=1
-ls /proc/cpuinfo >& /dev/null # very noddy attempt to figure out thread count
-if [ $? -eq 0 ]; then
-  CPU=`grep -c ^processor /proc/cpuinfo`
-else
-  CPU=`sysctl -a | grep machdep.cpu | grep thread_count | awk '{print $2}'`
-  if [ $? -ne 0 ]; then
-    # fall back to unthreaded core test
-    CPU=`sysctl -a | grep machdep.cpu | grep core_count | awk '{print $2}'`
-  fi
-fi
-if [ "$CPU" -gt "6" ]; then
-  CPU=6
+# ALL tool versions used by opt-build.sh
+# need to keep in sync with Dockerfile
+export VER_HTSLIB="1.10.2"
+export VER_LIBBW="0.4.2"
+
+if [[ ($# -ne 1 && $# -ne 2) ]] ; then
+  echo "Please provide an installation path and optionally perl lib paths to allow, e.g."
+  echo "  ./setup.sh /opt/myBundle"
+  echo "OR all elements versioned:"
+  echo "  ./setup.sh /opt/cgpPinel-X.X.X /opt/cgpVcf-X.X.X/lib/perl:/opt/PCAP-core-X.X.X/lib/perl"
+  exit 1
 fi
-echo "Max compilation CPUs set to $CPU"
-
-set -e
 
 INST_PATH=$1
 
+if [[ $# -eq 2 ]] ; then
+  CGP_PERLLIBS=$2
+fi
+
 # get current directory
 INIT_DIR=`pwd`
 
+set -e
+
 # cleanup inst_path
-mkdir -p $INST_PATH
+mkdir -p $INST_PATH/bin
 cd $INST_PATH
 INST_PATH=`pwd`
-mkdir -p $INST_PATH/bin
 cd $INIT_DIR
 
-#create a location to build dependencies
-SETUP_DIR=$INIT_DIR/install_tmp
-mkdir -p $SETUP_DIR
-
-echo -n "Get htslib ..."
-if [ -e $SETUP_DIR/htslibGet.success ]; then
-  echo " already staged ...";
-else
-  echo
-  cd $SETUP_DIR
-  get_distro "htslib" $SOURCE_HTSLIB
-  touch $SETUP_DIR/htslibGet.success
-fi
-
-echo -n "Building htslib ..."
-if [ -e $SETUP_DIR/htslib.success ]; then
-  echo " previously installed ...";
-else
-  echo
-  cd $SETUP_DIR
-  mkdir -p htslib
-  tar --strip-components 1 -C htslib -jxf htslib.tar.bz2
-  cd htslib
-  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
-  make -j$CPU
-  make install
-  rm -f $INST_PATH/lib/libhts.so*
-  cd $SETUP_DIR
-  touch $SETUP_DIR/htslib.success
-fi
-
-cd $INIT_DIR
-
-echo -n "Building libBigWig ..."
-if [ -e $SETUP_DIR/libBigWig.success ]; then
-  echo -n " previously installed ...";
-else
-  cd $SETUP_DIR
-  get_distro "libBigWig" $SOURCE_LIB_BW
-  mkdir -p libBigWig
-  tar --strip-components 1 -C libBigWig -zxf libBigWig.tar.gz
-  make -C libBigWig -j$CPU install prefix=$INST_PATH
-  rm -f $INST_PATH/lib/libBigWig.so
-  touch $SETUP_DIR/libBigWig.success
-fi
-echo
-
-export HTSLIB="$SETUP_DIR/htslib"
-cd $INIT_DIR
-
-
-echo -n "Building cgpBigWig ..."
-if [ -e $SETUP_DIR/cgpBigWig.success ]; then
-  echo -n " previously installed ...";
-else
-  cd $INIT_DIR
-  make -C c clean
-  make -C c -j$CPU prefix=$INST_PATH HTSLIB=$SETUP_DIR/htslib
-  cp bin/bam2bedgraph $INST_PATH/bin/.
-  cp bin/bwjoin $INST_PATH/bin/.
-  cp bin/bam2bw $INST_PATH/bin/.
-  cp bin/bwcat $INST_PATH/bin/.
-  cp bin/bam2bwbases $INST_PATH/bin/.
-  cp bin/bg2bw $INST_PATH/bin/.
-  cp bin/detectExtremeDepth $INST_PATH/bin/.
-  touch $SETUP_DIR/cgpBigWig.success
-  # need to clean up as will clash with other version
-  make -C c clean
-fi
-echo
+#add bin path for install tests
+export PATH=$INST_PATH/bin:$PATH
 
-# cleanup all junk
-rm -rf $SETUP_DIR
+bash build/opt-build.sh $INST_PATH
+bash build/opt-build-local.sh $INST_PATH
 
 echo
 echo