Merge branch 'release/1.17.0'

CHANGES.md

@@ -1,5 +1,11 @@
 # CHANGES
 
+## 1.17.0
+
+* Updated Dockerfile to use PCAP-core 5.2.2
+* Updated setup.sh script to remove redundant logic
+* Updated CaVEMan core to [1.15.0](https://github.com/cancerit/CaVEMan/releases/tag/1.15.0)
+
 ## 1.16.0
 
 * Pulls in cgpCaVEManPostProcessing 1.9.0

Dockerfile

@@ -1,23 +1,26 @@
-FROM  quay.io/wtsicgp/pcap-core:4.4.0 as builder
+FROM  quay.io/wtsicgp/pcap-core:5.2.2 as builder
 
 USER  root
 
 # ALL tool versions used by opt-build.sh
 ENV VER_VCFTOOLS="0.1.16"
 ENV VER_CGPVCF="v2.2.1"
-ENV VER_CAVEMAN="1.14.1"
+ENV VER_CAVEMAN="1.15.0"
 ENV VER_BEDTOOLS="2.27.1"
 ENV VER_CGPCAVEPOSTPROC="1.9.0"
 
 RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends \
-locales \
-g++ \
-make \
-gcc \
-pkg-config \
-python \
-zlib1g-dev
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends pkg-config
+RUN apt-get install -yq --no-install-recommends python
+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-openssl-dev
+
 
 RUN locale-gen en_US.UTF-8
 RUN update-locale LANG=en_US.UTF-8
@@ -38,16 +41,16 @@ 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" \
-      version="1.16.0" \
+      version="1.17.0" \
       description="cgpCaVEManWrapper docker"
 
+
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends \
-apt-transport-https \
 locales \
 curl \
 ca-certificates \
@@ -59,6 +62,10 @@ zlib1g \
 liblzma5 \
 libncurses5 \
 p11-kit \
+libcurl3-gnutls \
+libcurl4 \
+moreutils \
+google-perftools \
 unattended-upgrades && \
 unattended-upgrade -d -v && \
 apt-get remove -yq unattended-upgrades && \

lib/Sanger/CGP/Caveman.pm

@@ -26,6 +26,6 @@ package Sanger::CGP::Caveman;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '1.16.0';
+our $VERSION = '1.17.0';
 
 1;

setup.sh

@@ -21,115 +21,74 @@
 #  along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
 
-CAVEMAN_CORE="https://github.com/cancerit/CaVEMan/archive/1.14.1.tar.gz"
-
-get_distro () {
+# ALL tool versions used by opt-build.sh
+# need to keep in sync with Dockerfile
+export VER_VCFTOOLS="0.1.16"
+export VER_CGPVCF="v2.2.1"
+export VER_CAVEMAN="1.15.0"
+export VER_BEDTOOLS="2.27.1"
+export VER_CGPCAVEPOSTPROC="1.9.0"
+
+get_file () {
+# output, source
   if hash curl 2>/dev/null; then
-    curl -sS -o $1.tar.gz -L $2
+    curl -sS -o $1 -L $2
   else
-    wget -nv -O $1.tar.gz $2
+    wget -nv -O $1 $2
   fi
-  mkdir -p $1
-  tar --strip-components 1 -C $1 -zxf $1.tar.gz
 }
 
-if [ ! -z ${CAVE_C_REMOTE_TAR+x} ] ; then
-  CAVEMAN_CORE=$CAVE_C_REMOTE_TAR
-fi
 
-if [ "$#" -ne "1" ] ; then
-  echo "Please provide an installation path  such as /opt/ICGC"
-  exit 0
+if [[ ($# -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/cgpVcf-X.X.X /opt/PCAP-X.X.X/lib/perl:/some/other/lib/perl..."
+  exit 1
 fi
 
-CPU=`cat /proc/cpuinfo | egrep "^processor" | wc -l`
-echo "Max compilation CPUs set to $CPU"
-
 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/bin
 cd $INST_PATH
 INST_PATH=`pwd`
 cd $INIT_DIR
 
 # make sure that build is self contained
-unset PERL5LIB
-ARCHNAME=`perl -e 'use Config; print $Config{archname};'`
 PERLROOT=$INST_PATH/lib/perl5
-export PERL5LIB="$PERLROOT"
-
-#create a location to build dependencies
-SETUP_DIR=$INIT_DIR/install_tmp
-mkdir -p $SETUP_DIR
-
 
-# log information about this system
-echo '============== System information ===='
-set -x
-lsb_release -a
-uname -a
-sw_vers
-system_profiler
-grep MemTotal /proc/meminfo
-set +x
-echo
-
-CHK=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' PCAP`
-if [[ "x$CHK" == "x" ]] ; then
-  echo "PREREQUISITE: Please install PCAP-core before proceeding: https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases"
-  exit 1;
-fi
-
-
-if [ ! -e $PERLROOT/Sanger/CGP/CavemanPostProcessor.pm ]; then
-  echo "PREREQUISITE: Please install cgpCaVEManPostProcessing before proceeding: https://github.com/cancerit/cgpCaVEManPostProcessing/releases"
-  exit 1;
-fi
-
-
-echo -n "Building CaVEMan ..."
-if [ -e $SETUP_DIR/caveman.success ]; then
-  echo -n " previously installed ...";
+# allows user to knowingly specify other PERL5LIB areas.
+if [ -z ${CGP_PERLLIBS+x} ]; then
+  PERL5LIB="$PERLROOT"
 else
-  cd $SETUP_DIR
-  set -xe
-  if [ ! -e caveman ]; then
-    get_distro "caveman" $CAVEMAN_CORE
-  fi
-  cd caveman
-  ./setup.sh $INST_PATH
-  cp scripts/mergeCavemanResults $INST_PATH/bin/.
-  chmod a+x $INST_PATH/bin/mergeCavemanResults
-  touch $SETUP_DIR/caveman.success
+  PERL5LIB="$PERLROOT:$CGP_PERLLIBS"
 fi
 
-#add bin path for PCAP install tests
-export PATH="$INST_PATH/bin:$PATH"
+export PERL5LIB=$PERL5LIB
 
-cd $INIT_DIR
+#add bin path for install tests
+export PATH=$INST_PATH/bin:$PATH
 
-echo -n "Installing Perl prerequisites ..."
-if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
-  echo
-  echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."
-fi
-set -x
-perl $INIT_DIR/bin/cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH/ --installdeps . < /dev/null
-set +x
+#create a location to build dependencies
+SETUP_DIR=$INIT_DIR/install_tmp
+mkdir -p $SETUP_DIR
 
-echo -n "Installing cgpCaVEManWrapper ..."
-cd $INIT_DIR
-perl Makefile.PL INSTALL_BASE=$INST_PATH
-make
-make test
-make install
+#install cpanm
+get_file $SETUP_DIR/cpanm https://cpanmin.us/
+perl $SETUP_DIR/cpanm -l $INST_PATH App::cpanminus
 
-# cleanup all junk
-rm -rf $SETUP_DIR
+bash build/opt-build.sh $INST_PATH
+bash build/opt-build-local.sh $INST_PATH
 
 echo
 echo
@@ -138,3 +97,5 @@ echo "  $INST_PATH/bin"
 echo "Please add the following to beginning of PERL5LIB:"
 echo "  $PERLROOT"
 echo
+
+exit 0