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Merge pull request #70 from cancerit/develop
merge 3.5.1 into main
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,27 +1,43 @@ | ||
| FROM ubuntu:22.04 as builder | ||
| FROM ubuntu:18.04 as builder | ||
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| USER root | ||
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| # ALL tool versions used by opt-build.sh | ||
| ENV VER_SAMTOOLS="1.14" | ||
| ENV VER_HTSLIB="1.14" | ||
| ENV VER_BCFTOOLS="1.14" | ||
| ENV VER_SAMTOOLS="1.18" | ||
| ENV VER_HTSLIB="1.18" | ||
| ENV VER_BCFTOOLS="1.18" | ||
| ENV VER_VERIFYBAMID="2.0.1" | ||
| ENV VER_LIBDEFLATE="v1.12" | ||
| ENV VER_LIBDEFLATE="v1.18" | ||
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| ENV DEBIAN_FRONTEND=noninteractive | ||
| RUN apt-get -yq update | ||
| RUN apt-get install -yq --no-install-recommends locales | ||
| RUN apt-get install -yq --no-install-recommends g++ | ||
| RUN apt-get install -yq --no-install-recommends ca-certificates | ||
| RUN apt-get install -yq --no-install-recommends cmake | ||
| 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 | ||
| RUN apt-get install -yq --no-install-recommends software-properties-common lsb-release | ||
| 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 | ||
| RUN apt-add-repository "deb https://apt.kitware.com/ubuntu/ $(lsb_release -cs) main" | ||
| 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 | ||
| RUN apt-get install -yq --no-install-recommends bzip2 | ||
| RUN apt-get install -yq --no-install-recommends gcc | ||
| RUN apt-get install -yq --no-install-recommends pkg-config | ||
| RUN apt-get install -yq --no-install-recommends wget | ||
| RUN apt-get install -yq --no-install-recommends locales | ||
| RUN apt-get install -yq --no-install-recommends r-base | ||
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| # if ubuntu 18.04 | ||
| RUN apt install -yq --no-install-recommends dirmngr | ||
| 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 | ||
| RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" | ||
| RUN apt-get install -yq --no-install-recommends r-base-core=4.1.3-1.1804.0 | ||
| RUN apt-mark hold r-base-core | ||
| 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 | ||
| RUN apt-get install -yq --no-install-recommends r-recommended=4.1.3-1.1804.0 | ||
| RUN apt-get install -yq --no-install-recommends r-base=4.1.3-1.1804.0 | ||
| RUN apt-mark hold r-base r-recommended | ||
| # if ubuntu 22.04 | ||
| # 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 | ||
| RUN apt-get install -yq --no-install-recommends libbz2-dev | ||
| RUN apt-get install -yq --no-install-recommends liblzma-dev | ||
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@@ -57,11 +73,11 @@ RUN bash build/opt-build.sh $OPT | |
| COPY . . | ||
| RUN bash build/opt-build-local.sh $OPT | ||
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| FROM ubuntu:22.04 | ||
| FROM ubuntu:18.04 | ||
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| LABEL maintainer="[email protected]" \ | ||
| uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \ | ||
| version="1.0.0" \ | ||
| version="1.0.1" \ | ||
| description="nanoseq docker" | ||
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| ENV DEBIAN_FRONTEND=noninteractive | ||
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@@ -70,19 +86,21 @@ RUN apt-get install -yq --no-install-recommends \ | |
| apt-transport-https \ | ||
| locales \ | ||
| curl \ | ||
| wget \ | ||
| make \ | ||
| g++ \ | ||
| gcc \ | ||
| gfortran \ | ||
| libblas-dev \ | ||
| liblapack-dev \ | ||
| ca-certificates \ | ||
| time \ | ||
| zlib1g \ | ||
| libz-dev \ | ||
| python3 \ | ||
| r-base \ | ||
| r-cran-ggplot2 \ | ||
| r-cran-data.table \ | ||
| r-cran-epitools \ | ||
| r-cran-gridextra \ | ||
| r-cran-seqinr \ | ||
| libxml2 \ | ||
| libgsl27 \ | ||
| libperl5.34 \ | ||
| libgsl23 \ | ||
| libperl5.26 \ | ||
| libcapture-tiny-perl \ | ||
| libfile-which-perl \ | ||
| libpng16-16 \ | ||
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@@ -92,6 +110,18 @@ unattended-upgrade -d -v && \ | |
| apt-get remove -yq unattended-upgrades && \ | ||
| apt-get autoremove -yq | ||
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| RUN apt install -yq --no-install-recommends software-properties-common dirmngr | ||
| 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 | ||
| RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" | ||
| RUN apt-get install -yq --no-install-recommends r-base-core=4.1.3-1.1804.0 | ||
| RUN apt-mark hold r-base-core | ||
| 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 | ||
| RUN apt-get install -yq --no-install-recommends r-recommended=4.1.3-1.1804.0 | ||
| RUN apt-get install -yq --no-install-recommends r-base=4.1.3-1.1804.0 | ||
| RUN apt-mark hold r-base r-recommended | ||
| ADD build/libInstall2.R build/ | ||
| RUN Rscript build/libInstall2.R | ||
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| RUN locale-gen en_US.UTF-8 | ||
| RUN update-locale LANG=en_US.UTF-8 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| #!/usr/bin/env Rscript | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2022 Genome Research Ltd | ||
| # | ||
| # Author: CASM/Cancer IT <[email protected]> | ||
| # | ||
| # 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’. | ||
| ########################### | ||
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| #install R packages | ||
| install.packages(c("ggplot2", "data.table", "epitools", "gridExtra", "seqinr")) |
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