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Feature/r version (#69)
* update version * update r version * add cran * rm sudo * change r version * change r version again * ubuntu to 18 and garbage command * add R repos * yq * r version * r recommended * fix mistake * ubuntu 22 * r version * back to ubuntu 18 * cmake -S * cmake futility * update cmake * remove already-installed * update R version second install * update libgsl and libperl versions to match ubuntu 18.04 * include wget in second image * hold r versions * install R packages from script * add second R install script * add make * add gcc g++ * install gfortan, lapack, blas; fix spelling * garbage commit * garbage removed * add zlib-dev * update version --------- Co-authored-by: ab63 <[email protected]>
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‎CHANGES.md‎

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# CHANGES
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## 3.5.1
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* Dockerfile updated to avoid snv_merge_and_vaf_calc.R bug and to improve reproducibility
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* Small change to hardcoded overlapping_mask value in indel caller
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## 3.5.0
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* Minor bug in the indel pipeline fixed (was using bitwise OR instead of logical OR)
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* New quality metrics added to the indel calls such that SNVs and indels come out with the same metrics

‎Dockerfile‎

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FROM ubuntu:22.04 as builder
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FROM ubuntu:18.04 as builder
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USER root
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@@ -14,14 +14,30 @@ RUN apt-get -yq update
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RUN apt-get install -yq --no-install-recommends locales
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RUN apt-get install -yq --no-install-recommends g++
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RUN apt-get install -yq --no-install-recommends ca-certificates
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RUN apt-get install -yq --no-install-recommends cmake
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RUN apt-get install -yq --no-install-recommends wget
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# install latest cmake so opt-build.sh works - the initial installs will also help install R
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RUN apt-get install -yq --no-install-recommends software-properties-common lsb-release
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RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | tee /etc/apt/trusted.gpg.d/kitware.gpg >/dev/null
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RUN apt-add-repository "deb https://apt.kitware.com/ubuntu/ $(lsb_release -cs) main"
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RUN apt-get install -yq --no-install-recommends cmake=3.25.2-0kitware1ubuntu18.04.1
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RUN apt-get install -yq --no-install-recommends make
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RUN apt-get install -yq --no-install-recommends bzip2
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RUN apt-get install -yq --no-install-recommends gcc
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RUN apt-get install -yq --no-install-recommends pkg-config
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RUN apt-get install -yq --no-install-recommends wget
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RUN apt-get install -yq --no-install-recommends locales
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RUN apt-get install -yq --no-install-recommends r-base
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# if ubuntu 18.04
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RUN apt install -yq --no-install-recommends dirmngr
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RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
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RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
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RUN apt-get install -yq --no-install-recommends r-base-core=4.1.3-1.1804.0
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RUN apt-mark hold r-base-core
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RUN apt-get install -yq --no-install-recommends r-cran-mass=7.3-51.5-2bionic0 r-cran-class=7.3-16-1bionic0 r-cran-nnet=7.3-13-1bionic0
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RUN apt-get install -yq --no-install-recommends r-recommended=4.1.3-1.1804.0
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RUN apt-get install -yq --no-install-recommends r-base=4.1.3-1.1804.0
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RUN apt-mark hold r-base r-recommended
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# if ubuntu 22.04
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# RUN apt-get install -yq --no-install-recommends r-base=4.1.2-1ubuntu2
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RUN apt-get install -yq --no-install-recommends zlib1g-dev
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RUN apt-get install -yq --no-install-recommends libbz2-dev
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RUN apt-get install -yq --no-install-recommends liblzma-dev
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COPY . .
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RUN bash build/opt-build-local.sh $OPT
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FROM ubuntu:22.04
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FROM ubuntu:18.04
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LABEL maintainer="[email protected]" \
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uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
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version="1.0.0" \
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version="1.0.1" \
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description="nanoseq docker"
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ENV DEBIAN_FRONTEND=noninteractive
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apt-transport-https \
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locales \
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curl \
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wget \
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make \
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g++ \
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gcc \
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gfortran \
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libblas-dev \
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liblapack-dev \
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ca-certificates \
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time \
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zlib1g \
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libz-dev \
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python3 \
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r-base \
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r-cran-ggplot2 \
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r-cran-data.table \
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r-cran-epitools \
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r-cran-gridextra \
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r-cran-seqinr \
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libxml2 \
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libgsl27 \
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libperl5.34 \
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libgsl23 \
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libperl5.26 \
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libcapture-tiny-perl \
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libfile-which-perl \
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libpng16-16 \
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apt-get remove -yq unattended-upgrades && \
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apt-get autoremove -yq
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RUN apt install -yq --no-install-recommends software-properties-common dirmngr
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RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
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RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
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RUN apt-get install -yq --no-install-recommends r-base-core=4.1.3-1.1804.0
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RUN apt-mark hold r-base-core
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RUN apt-get install -yq --no-install-recommends r-cran-mass=7.3-51.5-2bionic0 r-cran-class=7.3-16-1bionic0 r-cran-nnet=7.3-13-1bionic0
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RUN apt-get install -yq --no-install-recommends r-recommended=4.1.3-1.1804.0
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RUN apt-get install -yq --no-install-recommends r-base=4.1.3-1.1804.0
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RUN apt-mark hold r-base r-recommended
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ADD build/libInstall2.R build/
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RUN Rscript build/libInstall2.R
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RUN locale-gen en_US.UTF-8
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RUN update-locale LANG=en_US.UTF-8
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‎build/libInstall2.R‎

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#!/usr/bin/env Rscript
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########## LICENCE ##########
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# Copyright (c) 2022 Genome Research Ltd
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#
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# Author: CASM/Cancer IT <[email protected]>
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#
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# This file is part of NanoSeq.
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Affero General Public License as
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# published by the Free Software Foundation, either version 3 of the
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# License, or (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Affero General Public License for more details.
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#
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# You should have received a copy of the GNU Affero General Public License
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# along with this program. If not, see <https://www.gnu.org/licenses/>.
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#
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# 1. The usage of a range of years within a copyright statement contained within
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# this distribution should be interpreted as being equivalent to a list of years
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# including the first and last year specified and all consecutive years between
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# them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
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# 2009, 2011-2012’ should be interpreted as being identical to a statement that
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# reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
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# statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
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# identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
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# 2009, 2010, 2011, 2012’.
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###########################
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#install R packages
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install.packages(c("ggplot2", "data.table", "epitools", "gridExtra", "seqinr"))

‎python/runNanoSeq.py‎

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import tempfile
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import copy
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version = '3.4.0'
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version = '3.5.1'
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parser = argparse.ArgumentParser()
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# arguments for all subcommands

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