Merge branch 'release/4.3.4'

CHANGES.md

@@ -1,5 +1,10 @@
 # Changes
 
+## 4.3.4
+
+* Eliminated redundant logic from setup script
+* Updated Dockerfile to use PCAP-core 5.2.1 as base (Ubuntu 20.04)
+
 ## 4.3.3
 
 * Add Rprofile to fix issues with scientific notation

Dockerfile

@@ -1,22 +1,21 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:3.1.4 as builder
+FROM quay.io/wtsicgp/pcap-core:5.2.1 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_BIODBHTS="2.10"
-#ENV VER_HTSLIB="1.7"
-ENV VER_ALLELECOUNT="v4.0.0"
+ENV VER_ALLELECOUNT="4.1.0"
 
 RUN apt-get -yq update
 
 RUN apt-get install -qy --no-install-recommends lsb-release
-
-RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/" >> /etc/apt/sources.list
+RUN apt-get install -qy --no-install-recommends gnupg
+RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`-cran40/" >> /etc/apt/sources.list
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 RUN apt-get -yq update
 
+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++
@@ -27,7 +26,8 @@ RUN apt-get install -yq --no-install-recommends pkg-config
 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 unzip
-RUN apt-get install -yq --no-install-recommends libpng12-dev
+RUN apt-get install -yq --no-install-recommends libpng-dev
+RUN apt-get install -yq --no-install-recommends tzdata
 RUN apt-get install -yq --no-install-recommends r-base
 RUN apt-get install -yq --no-install-recommends libcurl4-openssl-dev
 RUN apt-get install -yq --no-install-recommends libxml2-dev
@@ -63,9 +63,9 @@ COPY build/Rprofile $OPT/config/Rprofile
 # don't work in the default location, it can cause problems
 WORKDIR /tmp/builder
 
-COPY build/rlib-build.R build/
+COPY build/libInstall.R build/
 RUN mkdir -p $R_LIBS_USER
-RUN Rscript build/rlib-build.R $R_LIBS_USER 2>&1 | grep '^\*'
+RUN Rscript build/libInstall.R $R_LIBS_USER 2>&1 | grep '^\*'
 
 # build tools from other repos
 ADD build/opt-build.sh build/
@@ -76,17 +76,19 @@ 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="4.3.3" \
+      version="4.3.4" \
       description="Ascat NGS docker"
 
 RUN apt-get -yq update \
-&& apt-get install -qy --no-install-recommends lsb-release
+&& apt-get install -qy --no-install-recommends lsb-release \
+gnupg
 
-RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/" >> /etc/apt/sources.list \
+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 \
 && apt-get install -yq --no-install-recommends \
@@ -101,11 +103,14 @@ zlib1g \
 liblzma5 \
 libncurses5 \
 p11-kit \
+libcurl3-gnutls \
+libcurl4 \
+moreutils \
+google-perftools \
 libcairo2 \
 gfortran \
 r-base \
 time \
-r-base \
 unattended-upgrades && \
 unattended-upgrade -d -v && \
 apt-get remove -yq unattended-upgrades && \

build/libInstall.R

@@ -0,0 +1,55 @@
+instLib = commandArgs(T)[1]
+
+r = getOption("repos") # hard code the UK repo for CRAN
+r["CRAN"] = "http://cran.uk.r-project.org"
+options(repos = r)
+rm(r)
+
+ipak <- function(pkg){
+  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
+  if (length(new.pkg))
+    biocLite(new.pkg, ask=FALSE, lib=instLib, lib.loc=instLib)
+  sapply(pkg, library, character.only = TRUE)
+}
+
+ipak_bioc <- function(pkg){
+  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
+  if (length(new.pkg))
+    BiocManager::install(new.pkg, ask=FALSE, lib=instLib, lib.loc=instLib)
+  sapply(pkg, library, character.only = TRUE)
+}
+
+if( (version$major == 3 && version$minor >=5) || version$major > 3) {
+  # biocmanager versions of R
+  if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
+  BiocManager::install(ask=FALSE, lib=instLib, lib.loc=instLib)
+  ipak_bioc(c("data.table"))
+  ipak_bioc(c("gam"))
+  ipak_bioc(c("VGAM"))
+  ipak_bioc(c("stringr"))
+  ipak_bioc(c("mgcv"))
+  ipak_bioc(c("poweRlaw"))
+  ipak_bioc(c("zlibbioc"))
+  ipak_bioc(c("RColorBrewer"))
+} else {
+  # OLD versions of R
+  source("http://bioconductor.org/biocLite.R")
+  ipak(c("data.table"))
+  ipak(c("gam"))
+  if ( version$major == 3 && version$minor < 2 ) {
+    install.packages("VGAM_1.0-3.tar.gz", type="source", lib=instLib, lib.loc=instLib)
+  } else {
+    ipak(c("VGAM"))
+  }
+  ipak(c("stringr"))
+  ipak(c("mgcv"))
+  ipak(c("poweRlaw"))
+  ipak(c("zlibbioc"))
+  ipak(c("RColorBrewer"))
+}
+
+# works on old and new
+if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools", lib=instLib)
+library(devtools)
+options(download.file.method = "auto")
+install_github("Irrationone/copynumber", ref="87d2663fe6b11c03cf6006b4ee9ed70450eacb5a")

perl/bin/ascat.pl

@@ -53,7 +53,6 @@ BEGIN
   my $options = setup();
   Sanger::CGP::Ascat::Implement::prepare($options);
   my $threads = PCAP::Threaded->new($options->{'threads'});
-  &PCAP::Threaded::disable_out_err if(exists $options->{'index'});
 
   # register any process that can run in parallel here
   $threads->add_function('allele_count', \&Sanger::CGP::Ascat::Implement::allele_count);

setup.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
-########## LICENCE ##########
-# Copyright (c) 2014-2019 Genome Research Ltd.
+########## LICENSE ##########
+# Copyright (c) 2014-2020 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -19,15 +19,24 @@
 #
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
-########## LICENCE ##########
-
-# Update info in README.md if changed
-ASCAT_SRC="https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/v2.5.1/ASCAT/R/ascat.R"
-EXP_ACV="3.3.0"
+#
+#    1. The usage of a range of years within a copyright statement contained within
+#    this distribution should be interpreted as being equivalent to a list of years
+#    including the first and last year specified and all consecutive years between
+#    them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
+#    2009, 2011-2012’ should be interpreted as being identical to a statement that
+#    reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
+#    statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
+#    identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
+#    2009, 2010, 2011, 2012’."
+#
+###########################
 
-version_gt () {
-  test $(printf '%s\n' $@ | sort -V | head -n 1) == "$EXP_ACV";
-}
+# ALL tool versions used by opt-build.sh
+# 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"
 
 get_file () {
 # output, source
@@ -38,12 +47,13 @@ get_file () {
   fi
 }
 
+
 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 0
+  exit 1
 fi
 
 INST_PATH=$1
@@ -55,7 +65,7 @@ fi
 # get current directory
 INIT_DIR=`pwd`
 
-set -eu
+set -e
 
 # cleanup inst_path
 mkdir -p $INST_PATH/bin
@@ -82,84 +92,22 @@ export PATH=$INST_PATH/bin:$PATH
 SETUP_DIR=$INIT_DIR/install_tmp
 mkdir -p $SETUP_DIR
 
-cd $SETUP_DIR
-
-## grab cpanm and stick in workspace, then do a self upgrade into bin:
+#install cpanm
 get_file $SETUP_DIR/cpanm https://cpanmin.us/
 perl $SETUP_DIR/cpanm -l $INST_PATH App::cpanminus
-CPANM=`which cpanm`
-echo $CPANM
-
-PCAP=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' PCAP`
-if [[ "x$PCAP" == "x" ]] ; then
-  echo "PREREQUISITE: Please install PCAP-core before proceeding:"
-  echo "  https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases"
-  exit 1;
-fi
-
-AC=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::AlleleCount`
-if [[ "x$AC" == "x" ]] ; then
-  echo "PREREQUISITE: Please install alleleCount version >= $EXP_ACV before proceeding:"
-  echo "  https://github.com/cancerit/alleleCount/releases"
-  exit 1;
-else
-  if version_gt $AC $EXP_ACV; then
-    echo "  alleleCounter version is good ($AC)"
-  else
-    echo "PREREQUISITE: Please install alleleCount version >= $EXP_ACV before proceeding (Found version $AC):"
-    echo "  https://github.com/cancerit/alleleCount/releases"
-    exit 1;
-  fi
-fi
-
-VCF=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Vcf`
-if [[ "x$VCF" == "x" ]] ; then
-  echo "PREREQUISITE: Please install cgpVcf before proceeding:"
-  echo "  https://github.com/cancerit/cgpVcf/releases"
-  exit 1;
-fi
-
-HTS=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Bio::DB::HTS`
-if [[ "x$HTS" == "x" ]] ; then
-  echo "PREREQUISITE: Please install Bio::DB::HTS before proceeding:"
-  echo "  https://github.com/Ensembl/Bio-HTS/releases"
-  exit 1;
-fi
-
-perlmods=( "File::ShareDir" "File::ShareDir::Install" )
-
-for i in "${perlmods[@]}" ; do
-  echo "Installing build prerequisite $i..."
-  $CPANM -v --mirror http://cpan.metacpan.org -l $INST_PATH $i
-done
-
-cd $INIT_DIR/perl
-
-echo -n "Installing Perl prerequisites ..."
-if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
-    echo
-    echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."
-fi
-
-$CPANM -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH/ --installdeps . < /dev/null
-
-echo -n "Installing ascatNgs ..."
-get_file share/ascat/ascat.R $ASCAT_SRC
-perl Makefile.PL INSTALL_BASE=$INST_PATH
-make
-make test
-make install
-rm share/ascat/ascat.R
 
-# cleanup all junk
-rm -rf $SETUP_DIR
+#install R stuff
+export R_LIBS=$INST_PATH/R-libs
+export R_LIBS_USER=$INST_PATH/R-libs
+mkdir -p $R_LIBS_USER
+Rscript build/libInstall.R $R_LIBS_USER 2>&1 | grep '^\*'
+bash build/opt-build.sh $INST_PATH
+bash build/opt-build-local.sh $INST_PATH
 
 echo
 echo
 echo "Please add the following to beginning of path:"
 echo "  $INST_PATH/bin"
-echo "Please add the following to beginning of PERL5LIB:"
-echo "  $PERLROOT"
 echo
 
 exit 0