initial commit

Dockerfile

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+FROM  ubuntu:22.04 as builder
+
+USER  root
+
+
+ENV VER_LIBDEFLATE="v1.18"
+ENV VER_ISAL="v2.30.0"
+ENV VER_FASTP="v0.23.4"
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get -yq update --fix-missing
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get -y install wget
+RUN apt-get -y install make
+RUN apt-get -y install cmake
+RUN apt-get -y install autoconf
+RUN apt-get -y install libtool-bin
+RUN apt-get -y install nasm
+RUN apt-get -y install g++
+
+
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV R_LIBS $OPT/R-lib
+ENV R_LIBS_USER $R_LIBS
+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
+
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get -yq update --fix-missing
+RUN apt-get install -yq --no-install-recommends \
+locales 
+
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV R_LIBS $OPT/R-lib
+ENV R_LIBS_USER $R_LIBS
+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

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+# fastp
+container for fastp (v0.23.4)

build/opt-build.sh

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+#!/bin/bash
+
+########## LICENCE ##########
+# Copyright (c) 2022 Genome Research Ltd
+# 
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
+# 
+# This file is part of NanoSeq.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+# 
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# 
+# 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’.
+###########################
+
+
+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"
+  elif [[ $2 == *.tgz* ]] ; then
+    EXT="tgz"
+  else
+    echo "I don't understand the file type for $1"
+    exit 1
+  fi
+  rm -f $1.$EXT
+  if hash curl 2>/dev/null; then
+    curl --retry 10 -sS -o $1.$EXT -L $2
+  else
+    wget --tries=10 -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=`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"
+
+INST_PATH=$1
+
+# get current directory
+INIT_DIR=`pwd`
+
+set -e
+# cleanup inst_path
+mkdir -p $INST_PATH
+cd $INST_PATH
+INST_PATH=`pwd`
+mkdir -p $INST_PATH/bin
+cd $INIT_DIR
+
+export PATH="$INST_PATH/bin:$PATH"
+
+#create a location to build dependencies
+SETUP_DIR=$INIT_DIR/install_tmp
+mkdir -p $SETUP_DIR
+
+echo -n "Building libdeflate ..."
+if [ -e $SETUP_DIR/libdeflate.success ]; then
+  echo " previously built ...";
+else
+  echo
+  cd $SETUP_DIR
+  mkdir -p libdeflate
+  get_distro "libdeflate" "https://github.com/ebiggers/libdeflate/archive/${VER_LIBDEFLATE}.tar.gz"
+  tar --strip-components 1 -C libdeflate -zxf libdeflate.tar.gz
+  cd libdeflate
+  cmake -B build -DCMAKE_INSTALL_PREFIX:PATH=$INST_PATH && cmake --build build --target install
+  cd $SETUP_DIR
+  rm -r libdeflate.tar.gz
+  touch $SETUP_DIR/libdeflate.success
+fi
+
+echo -n "Building isa-l ..."
+if [ -e $SETUP_DIR/isa-l.success ]; then
+  echo " previously built ...";
+else
+  echo
+  cd $SETUP_DIR
+  mkdir -p isa-l
+  get_distro "isa-l" "https://github.com/intel/isa-l/archive/refs/tags/${VER_ISAL}.tar.gz"
+  tar --strip-components 1 -C isa-l -zxf isa-l.tar.gz
+  cd isa-l
+  ./autogen.sh
+  ./configure --prefix=$INST_PATH --libdir=$INST_PATH/lib
+  make
+  make install
+  cd $SETUP_DIR
+  rm -r isa-l.tar.gz
+  touch $SETUP_DIR/libdeflate.success
+fi
+
+echo -n "Building fastp ..."
+if [ -e $SETUP_DIR/fastp.success ]; then
+  echo " previously built ...";
+else
+  echo
+  cd $SETUP_DIR
+  mkdir -p fastp
+  get_distro "fastp" "https://github.com/OpenGene/fastp/archive/refs/tags/$VER_FASTP.tar.gz"
+  tar --strip-components 1 -C fastp -zxf fastp.tar.gz
+  cd fastp
+  export LD_FLAGS=-L$LD_LIBRARY_PATH
+  export PREFIX=$INST_PATH
+  make -j $CPU
+  make install
+  cd $SETUP_DIR
+  rm -r fastp.tar.gz
+  touch $SETUP_DIR/libdeflate.success
+fi