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Bootstrap: library | ||
From: nitishnarula/secure/ubuntu-focal:20210121 | ||
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%post | ||
export DEBIAN_FRONTEND=noninteractive | ||
# Updates | ||
apt-get update | ||
apt-get -y upgrade | ||
# Core tools | ||
# Beware tzdata prompts for input | ||
apt-get install -y tzdata | ||
apt-get install -y apt-utils | ||
apt-get install -y software-properties-common rsync | ||
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# ===== Tools====== | ||
apt-get install -y gnupg2 | ||
apt-get install -y tree | ||
apt-get install -y nano | ||
apt-get install -y git | ||
apt-get install -y wget | ||
apt-get install -y curl | ||
apt-get install -y pdftk | ||
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# ====== GH CLI ====== | ||
apt-key adv --keyserver keyserver.ubuntu.com --recv-key C99B11DEB97541F0 | ||
apt-add-repository https://cli.github.com/packages | ||
apt-get update | ||
apt-get install -y gh | ||
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#==========github============== | ||
curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash | ||
apt-get install -y git-lfs | ||
git lfs install | ||
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# ====== Markdown lint ====== | ||
apt-get install -y ruby | ||
gem install mdl | ||
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# ====== Python ====== | ||
apt-get install -y python3 | ||
apt-get install -y python3-pip | ||
pip3 install -U pytest | ||
apt-get install -y pep8 | ||
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# == Java=== | ||
apt-get install -y openjdk-14-jdk-headless | ||
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#======NPM===== | ||
apt-get install -y npm | ||
# npm i --save-dev eslint eslint-config-portsoc | ||
npm i eslint eslint-config-portsoc | ||
npm install log4js | ||
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# ===== Pandoc Stuff ====== | ||
apt-get install -y texlive-xetex | ||
apt-get install -y pandoc | ||
wget https://github.com/jgm/pandoc/releases/download/2.11.3.2/pandoc-2.11.3.2-1-amd64.deb | ||
dpkg -i pandoc-2.11.3.2-1-amd64.deb | ||
# For svg files | ||
apt-get install -y librsvg2-bin | ||
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#=========GO - Singularity========= | ||
wget https://dl.google.com/go/go1.15.11.linux-amd64.tar.gz | ||
tar -C /usr/local -xzvf go1.15.11.linux-amd64.tar.gz | ||
rm go1.15.11.linux-amd64.tar.gz | ||
echo 'export GOPATH=${HOME}/go' >> ~/.bashrc | ||
export GOPATH=${HOME}/go | ||
echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc | ||
export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin | ||
go version | ||
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#========== Singularity=========== | ||
cd /root | ||
wget https://github.com/hpcng/singularity/releases/download/v3.7.3/singularity-3.7.3.tar.gz | ||
tar -xzf singularity-3.7.3.tar.gz | ||
rm -f singularity-3.7.3.tar.gz | ||
cd singularity && \ | ||
./mconfig && \ | ||
make -C ./builddir && \ | ||
make -C ./builddir install | ||
rm -rf singularity/ | ||
singularity --version | ||
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# Clean up a bit | ||
apt-get clean |
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13
_recipes/cokelaer/damona/damona/software/helloworld/Singularity.helloworld_1.0.0
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BootStrap: docker | ||
From: alpine:3.8 | ||
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%post | ||
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apk update && apk add bash | ||
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%environment | ||
export PATH=/usr/local/bin:$PATH | ||
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%runscript | ||
echo "Hello Lenny" | ||
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33
_recipes/cokelaer/damona/damona/software/multiqc/Singularity.multiqc_1.16.0
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BootStrap: docker | ||
From: python:3.11-slim | ||
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%labels | ||
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AUTHOR Thomas Cokelaer | ||
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%files | ||
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sequana_0.16.0/ | ||
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%post | ||
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apt-get update | ||
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# force the version in case there is a pin on sequana | ||
pip install multiqc==1.16 | ||
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# this contains the multiqc modules only | ||
cp -r sequana_0.16.0 /opt | ||
cd /opt/sequana_0.16.0/sequana_0.16.0 | ||
pip install . | ||
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pip install colorlog | ||
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apt-get autoremove -y && apt-get clean | ||
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%environment | ||
export LANG=C.UTF-8 | ||
export LC_ALL=C.UTF-8 | ||
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40
_recipes/cokelaer/damona/damona/software/sequana/Singularity.sequana_0.16.1
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BootStrap: docker | ||
From: python:3.11-slim | ||
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%labels | ||
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AUTHOR Thomas Cokelaer | ||
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%post | ||
SAMTOOLS_VERSION=1.16 | ||
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apt-get update | ||
apt-get install -y wget make curl bzip2 build-essential | ||
apt-get install -y libhts-dev | ||
apt-get install -y graphviz | ||
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# to compile samtools | ||
apt install -y libncurses5-dev libbz2-dev | ||
# install samtools | ||
curl -sSL https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 | tar -xjf - \ | ||
&& cd samtools-$SAMTOOLS_VERSION \ | ||
&& ./configure && make && make install && cd - | ||
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# install htslib | ||
cd samtools-${SAMTOOLS_VERSION}/htslib-${SAMTOOLS_VERSION} && make && make install && cd - | ||
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rm -rf /samtools-$SAMTOOLS_VERSION | ||
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# Sequana source code | ||
pip install cython | ||
pip install sequana==0.16.1 | ||
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apt-get remove -y wget \ | ||
&& apt-get autoremove -y \ | ||
&& apt-get clean | ||
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%environment | ||
export LANG=C.UTF-8 | ||
export LC_ALL=C.UTF-8 | ||
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Bootstrap: docker | ||
From: ubuntu:20.04 | ||
IncludeCmd: yes | ||
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%labels | ||
MAINTAINER cschu ([email protected]) | ||
VERSION v.0.12 | ||
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%environment | ||
export LC_ALL=C | ||
export PATH=$PATH:/opt/software/bbmap/ | ||
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%post | ||
apt-get update | ||
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apt-get install -y | ||
apt-get install -y apt-transport-https apt-utils software-properties-common | ||
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apt-get install -y add-apt-key | ||
export DEBIAN_FRONTEND=noninteractive | ||
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime | ||
apt-get install -y tzdata | ||
dpkg-reconfigure --frontend noninteractive tzdata | ||
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apt-get install -y wget python3-pip git dirmngr gnupg ca-certificates build-essential libssl-dev libcurl4-gnutls-dev openjdk-11-jre | ||
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mkdir -p /opt/software/ && \ | ||
cd /opt/software && \ | ||
wget -O bbmap.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_39.03.tar.gz/download && \ | ||
tar xvzf bbmap.tar.gz && \ | ||
rm bbmap.tar.gz | ||
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Bootstrap: docker | ||
From: ubuntu:20.04 | ||
IncludeCmd: yes | ||
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%labels | ||
MAINTAINER cschu ([email protected]) | ||
VERSION v.0.12 | ||
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%environment | ||
export LC_ALL=C | ||
# export PATH=$PATH:/opt/software/prokka/bin:/opt/software/prokka/binaries/linux:/opt/software/miniconda3/bin | ||
# export PATH=$PATH:/opt/software/prokka/bin:/opt/software/miniconda3/bin | ||
export PATH=/opt/software/miniconda3/bin:$PATH | ||
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%post | ||
apt-get update | ||
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apt-get install -y | ||
apt-get install -y apt-transport-https apt-utils software-properties-common | ||
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apt-get install -y add-apt-key | ||
export DEBIAN_FRONTEND=noninteractive | ||
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime | ||
apt-get install -y tzdata | ||
dpkg-reconfigure --frontend noninteractive tzdata | ||
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apt-get install -y build-essential wget python3-pip git | ||
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wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \ | ||
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/software/miniconda3 && \ | ||
rm -f Miniconda3-latest-Linux-x86_64.sh && \ | ||
/opt/software/miniconda3/bin/conda install -y -c conda-forge -c bioconda diamond pyscipopt | ||
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# ls /opt/software/miniconda3/bin/ | ||
/opt/software/miniconda3/bin/pip install carveme | ||
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ln -s libscip.so.8.1.0.0 /opt/software/miniconda3/lib/libscip.so.8.0 | ||
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# echo ">protein1\nWHYYYYYYYYY" > dummy.faa | ||
# carve --solver scip dummy.faa | ||
export PATH=/opt/software/miniconda3/bin:$PATH | ||
diamond makedb --in /opt/software/miniconda3/lib/python3.11/site-packages/carveme/data/generated/bigg_proteins.faa -d /opt/software/miniconda3/lib/python3.11/site-packages/carveme/data/generated/bigg_proteins | ||
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31
_recipes/cschu/container-forge/Singularity.fish_probes.v0.1
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Bootstrap: docker | ||
From: ubuntu:20.04 | ||
IncludeCmd: yes | ||
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%labels | ||
MAINTAINER cschu ([email protected]) | ||
VERSION v.0.1 | ||
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%environment | ||
export LC_ALL=C | ||
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%post | ||
apt-get update | ||
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apt-get install -y | ||
apt-get install -y apt-transport-https apt-utils software-properties-common | ||
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apt-get install -y add-apt-key | ||
export DEBIAN_FRONTEND=noninteractive | ||
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime | ||
apt-get install -y tzdata | ||
dpkg-reconfigure --frontend noninteractive tzdata | ||
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apt-get install -y wget python3-pip git dirmngr gnupg ca-certificates build-essential libssl-dev libcurl4-gnutls-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev | ||
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pip3 install biopython | ||
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mkdir -p /opt/software | ||
git clone https://github.com/AlessioMilanese/FISH_probes.git | ||
cd FISH_probes | ||
pip3 install . |
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Bootstrap: docker | ||
From: ubuntu:20.04 | ||
IncludeCmd: yes | ||
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%labels | ||
MAINTAINER cschu ([email protected]) | ||
VERSION v.0.1 | ||
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%environment | ||
export LC_ALL=C | ||
export PATH=$PATH:/opt/software/miniconda3/bin:/opt/software/fetchMGs:/opt/software/fetchMGs/bin | ||
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%post | ||
apt-get update | ||
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apt-get install -y | ||
apt-get install -y apt-transport-https apt-utils software-properties-common | ||
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apt-get install -y add-apt-key | ||
export DEBIAN_FRONTEND=noninteractive | ||
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime | ||
apt-get install -y tzdata | ||
dpkg-reconfigure --frontend noninteractive tzdata | ||
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apt-get install -y wget python3-pip git dirmngr gnupg ca-certificates build-essential libssl-dev libcurl4-gnutls-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev | ||
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mkdir -p /opt/software && cd /opt/software | ||
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wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | ||
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/software/miniconda3 | ||
rm -f Miniconda3-latest-Linux-x86_64.sh | ||
/opt/software/miniconda3/bin/conda install -y -c conda-forge -c bioconda gffread>=0.11.6 | ||
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# # install what you can via conda | ||
# # /opt/software/miniconda3/bin/conda install -y -c conda-forge -c bioconda hmmer 'samtools>=1.13' bwa kraken2 'gatk4==4.1.6.0-0' fastqc multiqc bbmap seqtk | ||
# 'hmmer=3.3.2=h1b792b2_1' \ | ||
# 'samtools=1.13=h8c37831_0' \ | ||
# 'bwa=0.7.17=h5bf99c6_8' \ | ||
# 'kraken2=2.1.2=pl5262h7d875b9_0' \ | ||
# 'gatk4=4.1.6.0=py38_0' \ | ||
# 'fastqc=0.11.9=hdfd78af_1' \ | ||
# 'multiqc=1.11=pyhdfd78af_0' \ | ||
# 'bbmap=38.91=he522d1c_1' \ | ||
# 'seqtk=1.3=h5bf99c6_3' | ||
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Bootstrap: docker | ||
From: ubuntu:20.04 | ||
IncludeCmd: yes | ||
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%labels | ||
MAINTAINER cschu ([email protected]) | ||
VERSION v.0.1 | ||
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%environment | ||
export LC_ALL=C | ||
export PATH=$PATH:/opt/software/miniconda3/bin:/opt/software/fetchMGs:/opt/software/fetchMGs/bin | ||
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%post | ||
apt-get update | ||
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apt-get install -y | ||
apt-get install -y apt-transport-https apt-utils software-properties-common | ||
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apt-get install -y add-apt-key | ||
export DEBIAN_FRONTEND=noninteractive | ||
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime | ||
apt-get install -y tzdata | ||
dpkg-reconfigure --frontend noninteractive tzdata | ||
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apt-get install -y wget python3-pip git dirmngr gnupg ca-certificates build-essential libssl-dev libcurl4-gnutls-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev | ||
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mkdir -p /opt/software && cd /opt/software | ||
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wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | ||
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/software/miniconda3 | ||
rm -f Miniconda3-latest-Linux-x86_64.sh | ||
/opt/software/miniconda3/bin/conda install -y -c conda-forge -c bioconda bowtie2 diamond metaphlan | ||
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git clone https://github.com/biobakery/humann.git && cd humann && sed -i "363 s/3/4/" humann/config.py && sed -i "205 s/\$/.strip()/" humann/search/prescreen.py && sed -i '153i\ print(version_found)' humann/search/prescreen.py && sed -i "100 s/message/line/" humann/search/prescreen.py && /opt/software/miniconda3/bin/python setup.py install | ||
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# pip install humann | ||
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# # install what you can via conda | ||
# # /opt/software/miniconda3/bin/conda install -y -c conda-forge -c bioconda hmmer 'samtools>=1.13' bwa kraken2 'gatk4==4.1.6.0-0' fastqc multiqc bbmap seqtk | ||
# 'hmmer=3.3.2=h1b792b2_1' \ | ||
# 'samtools=1.13=h8c37831_0' \ | ||
# 'bwa=0.7.17=h5bf99c6_8' \ | ||
# 'kraken2=2.1.2=pl5262h7d875b9_0' \ | ||
# 'gatk4=4.1.6.0=py38_0' \ | ||
# 'fastqc=0.11.9=hdfd78af_1' \ | ||
# 'multiqc=1.11=pyhdfd78af_0' \ | ||
# 'bbmap=38.91=he522d1c_1' \ | ||
# 'seqtk=1.3=h5bf99c6_3' | ||
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