Merge branch 'release/1.1.0'

.dockerignore

@@ -0,0 +1,7 @@
+/LICENCE
+/README.md
+/INSTALL.md
+/LICENCE
+/CHANGES.md
+/.gitignore
+/.git

.travis.yml

@@ -2,46 +2,21 @@ notifications:
   slack: wtsi-cgpit:ptUMR1tkNyZJYd9TpGoss8WR
   email: false
 
-env:
-  - CC=gcc
+sudo: false
 
-language:
-  - c
-
-dist: trusty
-
-addons:
-  apt:
-    packages:
-      - build-essential
-      - curl
-      - libcurl4-openssl-dev
-      - libssl-dev
-      - nettle-dev
-      - zlib1g-dev
-      - libbz2-dev
-      - liblzma-dev
-
-install: true
+services:
+  - docker
 
 script:
-  - ./setup.sh ~/wtsi-opt
-
-matrix:
-  include:
-    - #Trusty
-      compiler: gcc
-      os: linux
-      sudo: required
-    - #Trusty
-      compiler: clang
-      os: linux
-      sudo: required
-    - dist: precise
-      compiler: gcc
-      os: linux
-      sudo: required
-    - dist: precise
-      compiler: clang
-      os: linux
-      sudo: required
+ - set -e
+ - echo 'Build and check docker image'
+ - docker build -t cgpbigwig .
+ - docker images | grep -c cgpbigwig
+ - echo 'Verify program(s) from this repo'
+ - docker run -t --rm cgpbigwig bam2bedgraph --version
+ - docker run -t --rm cgpbigwig bwjoin --version
+ - docker run -t --rm cgpbigwig bam2bw --version
+ - docker run -t --rm cgpbigwig bwcat --version
+ - docker run -t --rm cgpbigwig bam2bwbases --version
+ - docker run -t --rm cgpbigwig bg2bw --version
+ - docker run -t --rm cgpbigwig detectExtremeDepth --version

CHANGES.md

@@ -1,5 +1,10 @@
 # CHANGES
 
+## 1.1.0
+
+Add docker build to allow internal large CI system to process. dockstore-cgpbigwig will
+be modified to base from here and only contain additional helpers and CWL.
+
 ## 1.0.4
 
 * Add checks to sam_iter_next to ensure result is checked for errors
@@ -14,7 +19,7 @@
 * Where a proper pair filter is used, now check for the correct paired-end orientation of F/R.
 * If this is not met the read is ignored
 * Added a -f filter of flags to **include** alongside the existing -F for exclude as per samtools style filtering for `bam2bw`, `bam2bwbases` and `bam2bedgraph`
-* **NB this flag was used as the exclude in `bam2bedgraph`. The flags have now been switched.** 
+* **NB this flag was used as the exclude in `bam2bedgraph`. The flags have now been switched.**
 
 ## 1.0.2
 

Dockerfile

@@ -0,0 +1,78 @@
+FROM  ubuntu:16.04 as builder
+
+USER  root
+
+ARG VER_HTSLIB="1.9"
+ARG VER_LIBBW="0.4.2"
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+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 mkdir -p $OPT/bin
+
+WORKDIR /install_tmp
+
+ADD build/opt-build.sh build/
+RUN bash build/opt-build.sh $OPT
+
+COPY . .
+RUN bash build/opt-build-local.sh $OPT
+
+FROM  ubuntu:16.04
+
+LABEL maintainer="[email protected]"\
+      uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
+      version="1.1.0" \
+      description="cgpBigWig"
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL C
+
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends \
+apt-transport-https \
+curl \
+ca-certificates \
+bzip2 \
+zlib1g \
+liblzma5 \
+libncurses5 \
+unattended-upgrades && \
+unattended-upgrade -d -v && \
+apt-get remove -yq unattended-upgrades && \
+apt-get autoremove -yq
+
+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

@@ -2,22 +2,24 @@
 
 Package of C scripts for generation of [BigWig][BigWig] coverage files
 
+[![Quay Badge][quay-status]][quay-repo]
+
 | Master                                        | Dev                                          |
 |-----------------------------------------------|----------------------------------------------|
 | [![Master Badge][travis-master]][travis-base] |  [![Dev Badge][travis-develop]][travis-base] |
 
 <!-- TOC depthFrom:2 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->
 
-- [Installation](#installation)
-- [Docker and Singularity](#docker-and-singularity)
-- [Programs](#programs)
-	- [bwcat](#bwcat)
-	- [bwjoin](#bwjoin)
-	- [bam2bw](#bam2bw)
-	- [bg2bw](#bg2bw)
-	- [bam2bwbases](#bam2bwbases)
-	- [bam2bedgraph](#bam2bedgraph)
-- [License](#license)
+* [Installation](#installation)
+* [Docker and Singularity](#docker-and-singularity)
+* [Programs](#programs)
+	* [bwcat](#bwcat)
+	* [bwjoin](#bwjoin)
+	* [bam2bw](#bam2bw)
+	* [bg2bw](#bg2bw)
+	* [bam2bwbases](#bam2bwbases)
+	* [bam2bedgraph](#bam2bedgraph)
+* [License](#license)
 
 <!-- /TOC -->
 
@@ -38,6 +40,8 @@ To install this package run:
 
 ## Docker and Singularity
 
+A docker image for this tool can be found at [quay.io][quay-repo] (this may be more current than the dockstore version).
+
 There are [docker][quay.io] and [dockstore.org][dockstore] wrappers for this project at [dockstore-cgpbigwig] including CWL bindings.
 
 See the [dockstore-cgpbigwig] documentation for more detail.
@@ -204,3 +208,8 @@ identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
 [travis-master]: https://travis-ci.org/cancerit/cgpBigWig.svg?branch=master
 [travis-develop]: https://travis-ci.org/cancerit/cgpBigWig.svg?branch=develop
 [travis-base]: https://travis-ci.org/cancerit/cgpBigWig
+
+<!-- Quay.io -->
+[quay-status]: https://quay.io/repository/wtsicgp/cgpbigwig/status
+[quay-repo]: https://quay.io/repository/wtsicgp/cgpbigwig
+[quay-builds]: https://quay.io/repository/wtsicgp/cgpbigwig?tab=builds

VERSION.txt

@@ -1 +1 @@
-1.0.4
+1.1.0

build/opt-build-local.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+set -ex
+
+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"
+
+mkdir -p $INST_PATH/bin
+
+# 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:$MANPATH | perl -pe 's/:\$//;'`
+set -u
+
+##### cgpBigWig installation
+make -C c clean
+make -C c -j$CPU prefix=$INST_PATH HTSLIB=$INST_PATH/lib
+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/.
+make -C c clean
+
+cd $HOME

build/opt-build.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+
+set -ex
+
+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/:\$//;'`
+set -u
+
+##### DEPS for cgpBigWig #####
+
+## HTSLIB (tar.bz2)
+if [ ! -e $SETUP_DIR/htslib.success ]; then
+  rm -rf htslib
+  mkdir -p htslib
+  curl -sSL --retry 10 https://github.com/samtools/htslib/releases/download/${VER_HTSLIB}/htslib-${VER_HTSLIB}.tar.bz2 > distro.tar.bz2
+  tar --strip-components 1 -C htslib -jxf distro.tar.bz2
+  cd htslib
+  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
+  make clean
+  make -j$CPU
+  make install
+  cd $SETUP_DIR
+  rm -rf distro.*
+  touch $SETUP_DIR/htslib.success
+fi
+
+## LIB-BW (tar.gz)
+if [ ! -e $SETUP_DIR/libBigWig.success ]; then
+  curl -sSL --retry 10 https://github.com/dpryan79/libBigWig/archive/${VER_LIBBW}.tar.gz > distro.tar.gz
+  rm -rf distro/*
+  tar --strip-components 1 -C distro -xzf distro.tar.gz
+  make -C distro clean
+  make -C distro -j$CPU install prefix=$INST_PATH
+  rm -rf distro.* distro/*
+  touch $SETUP_DIR/libBigWig.success
+fi
+
+cd $HOME
+rm -rf $SETUP_DIR