From cc8b8d32d772706071ce98bbe8bfbba81ae1ba3c Mon Sep 17 00:00:00 2001
From: whalleyt <whalleyt@cardiff.ac.uk>
Date: Tue, 21 Nov 2023 18:11:54 +0000
Subject: [PATCH] permissions

---
 docker/Dockerfile.preprocessing-0.9.7r4 | 132 ++++++++++++++++++++++++
 nextflow.config                         |   6 +-
 2 files changed, 135 insertions(+), 3 deletions(-)
 create mode 100644 docker/Dockerfile.preprocessing-0.9.7r4

diff --git a/docker/Dockerfile.preprocessing-0.9.7r4 b/docker/Dockerfile.preprocessing-0.9.7r4
new file mode 100644
index 0000000..89267fc
--- /dev/null
+++ b/docker/Dockerfile.preprocessing-0.9.7r4
@@ -0,0 +1,132 @@
+FROM ubuntu:focal
+
+LABEL maintainer="pricea35@cardiff.ac.uk" \
+about.summary="container for the preprocessing workflow"
+
+ENV samtools_version=1.12 \
+bcftools_version=1.12 \
+htslib_version=1.12 \
+bedtools_version=2.29.2 \
+bowtie2_version=2.4.2 \
+fastp_version=0.20.1 \
+fastqc_version=0.11.9 \
+fqtools_version=2.3 \
+kraken2_version=2.1.1 \
+afanc_version=0.10.2 \
+mykrobe_version=0.12.1 \
+bwa_version=0.7.17 \
+mash_version=2.3 \
+fastani_version=1.33
+
+ENV PACKAGES="procps curl git wget build-essential zlib1g-dev libncurses-dev libz-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libgsl-dev rsync unzip ncbi-blast+ pigz jq libtbb-dev openjdk-11-jre-headless autoconf r-base-core locales locales-all" \
+PYTHON="python3 python3-pip python3-dev" \
+PYTHON_PACKAGES="biopython awscli boto3"
+
+ENV PATH=${PATH}:/usr/local/bin/mccortex/bin:/usr/local/bin/bwa-${bwa_version}:/opt/edirect \
+LD_LIBRARY_PATH=/usr/local/lib
+
+RUN export DEBIAN_FRONTEND="noninteractive"
+
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
+
+RUN apt-get update \
+&& DEBIAN_FRONTEND="noninteractive" apt-get install -y $PACKAGES $PYTHON \
+&& pip3 install --upgrade pip \
+&& pip3 install $PYTHON_PACKAGES \
+&& ln -s /usr/bin/python3 /usr/bin/python
+
+RUN curl -fsSL https://github.com/samtools/samtools/archive/${samtools_version}.tar.gz | tar -xz \
+&& curl -fsSL https://github.com/samtools/htslib/releases/download/${htslib_version}/htslib-${htslib_version}.tar.bz2 | tar -xj \
+&& make -C samtools-${samtools_version} -j HTSDIR=../htslib-${htslib_version} \
+&& make -C samtools-${samtools_version} -j HTSDIR=../htslib-${htslib_version} prefix=/usr/local install \
+&& rm -r samtools-${samtools_version} \
+&& curl -fsSL https://github.com/samtools/bcftools/archive/refs/tags/${bcftools_version}.tar.gz | tar -xz \
+&& make -C bcftools-${bcftools_version} -j HTSDIR=../htslib-${htslib_version} \
+&& make -C bcftools-${bcftools_version} -j HTSDIR=../htslib-${htslib_version} prefix=/usr/local install \
+&& rm -r bcftools-${bcftools_version}
+
+RUN curl -fsSL https://github.com/alastair-droop/fqtools/archive/v${fqtools_version}.tar.gz | tar -xz \
+&& mv htslib-${htslib_version} fqtools-${fqtools_version} \
+&& cd fqtools-${fqtools_version} \
+&& mv htslib-${htslib_version} htslib \
+&& cd htslib \
+&& autoreconf -i \
+&& ./configure \
+&& make \
+&& make install \
+&& cd .. \
+&& make \
+&& mv bin/* /usr/local/bin \
+&& chmod +x /usr/local/bin/fqtools \
+&& cd .. \
+&& rm -r fqtools-${fqtools_version}
+
+RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v${bedtools_version}/bedtools-${bedtools_version}.tar.gz | tar -xz \
+&& make -C bedtools2 \
+&& mv bedtools2/bin/* /usr/local/bin \
+&& rm -r bedtools2
+
+RUN curl -fsSL https://sourceforge.net/projects/bowtie-bio/files/bowtie2/${bowtie2_version}/bowtie2-${bowtie2_version}-source.zip -o bowtie2-${bowtie2_version}-source.zip \
+&& unzip bowtie2-${bowtie2_version}-source.zip \
+&& make -C bowtie2-${bowtie2_version} prefix=/usr/local install \
+&& rm -r bowtie2-${bowtie2_version} \
+&& rm bowtie2-${bowtie2_version}-source.zip
+
+RUN curl -fsSL https://github.com/OpenGene/fastp/archive/v${fastp_version}.tar.gz | tar -xz \
+&& cd fastp-${fastp_version} \
+&& make \
+&& make install \
+&& cd .. \
+&& rm -r fastp-${fastp_version}
+
+RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${fastqc_version}.zip \
+&& unzip fastqc_v${fastqc_version}.zip \
+&& chmod +x FastQC/fastqc \
+&& mv FastQC/* /usr/local/bin \
+&& rm fastqc_v${fastqc_version}.zip \
+&& rm -r FastQC
+
+RUN curl -fsSL https://github.com/DerrickWood/kraken2/archive/v${kraken2_version}.tar.gz | tar -xz \
+&& cd kraken2-${kraken2_version} \
+&& ./install_kraken2.sh /usr/local/bin \
+&& cd ..
+
+RUN curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_version}-alpha.tar.gz | tar -xz \
+&& cd Afanc-${afanc_version}-alpha \
+&& pip3 install ./ \
+&& cd .. \
+&& curl -fsSL "https://github.com/marbl/Mash/releases/download/v${mash_version}/mash-Linux64-v${mash_version}.tar" | tar -x \
+&& mv mash-Linux64-v${mash_version}/mash /usr/local/bin \
+&& rm -r mash-Linux* \
+&& wget https://github.com/ParBLiSS/FastANI/releases/download/v${fastani_version}/fastANI-Linux64-v${fastani_version}.zip \
+&& unzip fastANI-Linux64-v${fastani_version}.zip \
+&& mv fastANI /usr/local/bin
+
+RUN sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
+&& mkdir -p /opt/edirect \
+&& mv /root/edirect/* /opt/edirect
+
+RUN git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex \
+&& make -C mccortex \
+&& mv mccortex /usr/local/bin \
+&& curl -fsSL mykrobe-${mykrobe_version}.tar.gz https://github.com/Mykrobe-tools/mykrobe/archive/v${mykrobe_version}.tar.gz | tar -xz \
+&& cd mykrobe-${mykrobe_version} \
+&& pip3 install requests \
+&& pip3 install . \
+&& ln -s /usr/local/bin/mccortex/bin/mccortex31 /usr/local/lib/python3.8/dist-packages/mykrobe/cortex/mccortex31 \
+&& mykrobe panels update_metadata \
+&& mykrobe panels update_species all \
+&& cd ..
+
+RUN curl -fsSL https://github.com/lh3/bwa/archive/v${bwa_version}.tar.gz | tar -C /usr/local/bin -xz \
+&& make -C /usr/local/bin/bwa-${bwa_version} \
+&& chmod +x /usr/local/bin/bwa-${bwa_version}/bwa
+
+RUN unset DEBIAN_FRONTEND
+
+ENV LC_ALL en_US.UTF-8 \
+LANG en_US.UTF-8 \
+LANGUAGE en_US.UTF-8
+
diff --git a/nextflow.config b/nextflow.config
index 9744744..ef42345 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -90,7 +90,7 @@ profiles {
       withLabel:high_memory { memory = '18GB' }
 
       withLabel:preprocessing {
-        container = "quay.io/pathogen-genomics-cymru/preprocessing:0.9.7r2"
+        container = "quay.io/pathogen-genomics-cymru/preprocessing:0.9.7r4"
       }
       
       withLabel:getversion{
@@ -111,11 +111,11 @@ profiles {
       }
 
        withLabel:clockwork {
-        container = "quay.io/pathogen-genomics-cymru/clockwork:0.9.7r2"
+        container = "quay.io/pathogen-genomics-cymru/clockwork:0.9.7r3"
       }
 
       withLabel:vcfpredict {
-        container = "quay.io/pathogen-genomics-cymru/vcfpredict:0.9.7r2"
+        container = "quay.io/pathogen-genomics-cymru/vcfpredict:0.9.7r3"
       }
     }
       params{