Merge branch 'release/4.1.0'

Release with Docker files to build a container

.travis.yml

@@ -2,29 +2,17 @@ notifications:
   slack: wtsi-cgpit:ptUMR1tkNyZJYd9TpGoss8WR
   email: false
 
-env:
- - CC=gcc
+sudo: false
 
-addons:
- apt:
-  packages:
-   - build-essential
-   - autoconf
-   - curl
-   - zlib1g-dev
-   - libncurses5-dev
-   - libpstreams-dev
-   - libcurl4-openssl-dev
+language: ruby
 
-install: true
-
-language: perl
-
-perl:
- - "5.22"
-# - "5.16"
+services:
+  - docker
 
 script:
- - ./setup.sh $HOME/wtsi-opt
- - ls -l $HOME/wtsi-opt/bin/alleleCounter
- - ls -l $HOME/wtsi-opt/bin/alleleCounter.pl
+ - echo 'Build and check docker image'
+ - docker build -t allelec .
+ - docker images | grep -c allelec
+ - echo 'Verify program(s) from this repo'
+ - docker run -t --rm allelec alleleCounter -v
+ - docker run -t --rm allelec alleleCounter.pl -v

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## v4.1.0
+
+* Created Docker file and build scripts to generate a containeraized code
+
 ## v4.0.2
 
 * Added checking of iterator error codes when calling sam_itr_next

Dockerfile

@@ -0,0 +1,94 @@
+FROM  ubuntu:16.04 as builder
+
+USER  root
+
+# ALL tool versions used by opt-build.sh
+ENV VER_HTSLIB="1.7"
+
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends \
+build-essential \
+apt-transport-https \
+curl \
+ca-certificates \
+make \
+bzip2 \
+gcc \
+locales \
+curl \
+wget \
+libtasn1-dev \
+libgnutls-dev \
+nettle-dev \
+libgmp-dev \
+libp11-kit-dev \
+zlib1g-dev \
+libbz2-dev \
+liblzma-dev \
+libcurl4-gnutls-dev \
+libncurses5-dev
+
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+
+# build tools from other repos
+ADD build/opt-build.sh build/
+RUN bash build/opt-build.sh $OPT
+
+# build the tools in this repo, separate to reduce build time on errors
+COPY . .
+RUN bash build/opt-build-local.sh $OPT
+
+FROM ubuntu:16.04
+
+LABEL maintainer="cgphelp@sanger.ac.uk" \
+      uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
+      version="v1.0.0" \
+      description="alleleCount docker"
+
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends \
+apt-transport-https \
+locales \
+curl \
+ca-certificates \
+libperlio-gzip-perl \
+bzip2 \
+psmisc \
+time \
+zlib1g \
+liblzma5 \
+libncurses5 \
+p11-kit \
+unattended-upgrades && \
+unattended-upgrade -d -v && \
+apt-get remove -yq unattended-upgrades && \
+apt-get autoremove -yq
+
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+
+RUN mkdir -p $OPT
+COPY --from=builder $OPT $OPT
+
+## USER CONFIGURATION
+RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
+
+USER    ubuntu
+WORKDIR /home/ubuntu
+
+CMD ["/bin/bash"]

README.md

@@ -3,6 +3,8 @@
 The alleleCount package primarily exists to prevent code duplication between some other projects,
 specifically AscatNGS and Battenberg.
 
+[![Quay Badge][quay-status]][quay-repo]
+
 | Master                                        | Develop                                         |
 | --------------------------------------------- | ----------------------------------------------- |
 | [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |
@@ -160,3 +162,8 @@ identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
 
 <!-- refs -->
 [ds-cgpwgs-git]: https://github.com/cancerit/dockstore-cgpwgs
+
+<!-- Quay.io -->
+[quay-status]: https://quay.io/repository/wtsicgp/allelecount/status
+[quay-repo]: https://quay.io/repository/wtsicgp/allelecount
+[quay-builds]: https://quay.io/repository/wtsicgp/allelecount?tab=builds

build/opt-build-local.sh

@@ -0,0 +1,72 @@
+#! /bin/bash
+
+set -xe
+
+if [[ -z "${TMPDIR}" ]]; then
+  TMPDIR=/tmp
+fi
+
+set -u
+
+if [ "$#" -lt "1" ] ; then
+  echo "Please provide an installation path such as /opt/ICGC"
+  exit 1
+fi
+
+# get path to this script
+SCRIPT_PATH=`dirname $0`;
+SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)`
+
+# get the location to install to
+INST_PATH=$1
+mkdir -p $1
+INST_PATH=`(cd $1 && pwd)`
+echo $INST_PATH
+
+# get current directory
+INIT_DIR=`pwd`
+
+CPU=`grep -c ^processor /proc/cpuinfo`
+if [ $? -eq 0 ]; then
+  if [ "$CPU" -gt "6" ]; then
+    CPU=6
+  fi
+else
+  CPU=1
+fi
+echo "Max compilation CPUs set to $CPU"
+
+SETUP_DIR=$INIT_DIR/install_tmp
+mkdir -p $SETUP_DIR/distro # don't delete the actual distro directory until the very end
+mkdir -p $INST_PATH/bin
+cd $SETUP_DIR
+
+# make sure tools installed can see the install loc of libraries
+set +u
+export LD_LIBRARY_PATH=`echo $INST_PATH/lib:$LD_LIBRARY_PATH | perl -pe 's/:\$//;'`
+export PATH=`echo $INST_PATH/bin:$PATH | perl -pe 's/:\$//;'`
+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/:\$//;'`
+CPANM=`which cpanm`
+echo  "Installing Perl prerequisites ..."
+$CPANM --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH/ --installdeps $INIT_DIR/perl/. < /dev/null
+
+set -u
+### alleleCount
+echo "Building alleleCounter ..."
+if [ ! -e $SETUP_DIR/alleleCount.success ]; then
+  #build the C part
+  cd $INIT_DIR
+  mkdir -p $INIT_DIR/c/bin
+  make -C c clean
+  export prefix=$INST_PATH
+  make -C c -j$CPU
+  cp $INIT_DIR/c/bin/alleleCounter $INST_PATH/bin/.
+  #build the perl part
+  cd $INIT_DIR/perl
+  perl Makefile.PL INSTALL_BASE=$INST_PATH
+  make
+  make test
+  make install
+  touch $SETUP_DIR/alleleCounter.success
+fi

build/opt-build.sh

@@ -0,0 +1,86 @@
+#! /bin/bash
+
+set -xe
+
+if [[ -z "${TMPDIR}" ]]; then
+  TMPDIR=/tmp
+fi
+
+set -u
+
+if [ "$#" -lt "1" ] ; then
+  echo "Please provide an installation path such as /opt/ICGC"
+  exit 1
+fi
+
+# get path to this script
+SCRIPT_PATH=`dirname $0`;
+SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)`
+
+# get the location to install to
+INST_PATH=$1
+mkdir -p $1
+INST_PATH=`(cd $1 && pwd)`
+echo $INST_PATH
+
+# get current directory
+INIT_DIR=`pwd`
+
+CPU=`grep -c ^processor /proc/cpuinfo`
+if [ $? -eq 0 ]; then
+  if [ "$CPU" -gt "6" ]; then
+    CPU=6
+  fi
+else
+  CPU=1
+fi
+echo "Max compilation CPUs set to $CPU"
+
+SETUP_DIR=$INIT_DIR/install_tmp
+mkdir -p $SETUP_DIR/distro # don't delete the actual distro directory until the very end
+mkdir -p $INST_PATH/bin
+cd $SETUP_DIR
+
+# make sure tools installed can see the install loc of libraries
+set +u
+export LD_LIBRARY_PATH=`echo $INST_PATH/lib:$LD_LIBRARY_PATH | perl -pe 's/:\$//;'`
+export PATH=`echo $INST_PATH/bin:$PATH | perl -pe 's/:\$//;'`
+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
+
+## grab cpanm 
+curl -L http://cpanmin.us | perl - App::cpanminus
+CPANM=`which cpanm`
+
+echo "Installing Perl base deps ..."
+if [ ! -e $SETUP_DIR/basePerlDeps.success ]; then
+  perlmods=( "ExtUtils::CBuilder" "Module::Build~0.42" "Const::Fast" "File::Which" "LWP::UserAgent")
+  for i in "${perlmods[@]}" ; do
+    $CPANM --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
+  done
+  touch $SETUP_DIR/basePerlDeps.success
+fi
+
+SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/${VER_HTSLIB}/htslib-${VER_HTSLIB}.tar.bz2"
+
+cd $SETUP_DIR
+
+echo "Downloading htslib ..."
+if [ ! -e $SETUP_DIR/htslibGet.success ]; then
+  cd $SETUP_DIR
+  wget $SOURCE_HTSLIB
+  touch $SETUP_DIR/htslibGet.success
+fi
+
+echo "Building htslib ..."
+if [ ! -e $SETUP_DIR/htslib.success ]; then
+  mkdir -p htslib
+  tar --strip-components 1 -C htslib -jxf htslib-${VER_HTSLIB}.tar.bz2
+  cd htslib
+  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
+  make -j$CPU
+  make install
+  cd $SETUP_DIR
+  touch $SETUP_DIR/htslib.success
+fi

c/Makefile

@@ -12,7 +12,7 @@ CFLAGS = -g -Wall
 HTSLOC?=$(HTSLIB)
 
 HTSTMP?=./htslib_tmp
-prefix=?/usr/local/
+prefix?=/usr/local/
 
 #Define locations of header files
 OPTINC?=-I$(HTSLOC)/

perl/lib/Sanger/CGP/AlleleCount.pm

@@ -25,7 +25,7 @@ package Sanger::CGP::AlleleCount;
 use strict;
 
 use base 'Exporter';
-our $VERSION = '4.0.2';
+our $VERSION = '4.1.0';
 our @EXPORT = qw($VERSION);
 
 1;