Bootstrap: docker From: ubuntu:20.04 %labels MAINTAINER Julie Orjuela, François Sabot, Gautier Sarah version="1.0" %environment export PATH="${PATH}:/usr/local/miniconda/miniconda3/envs/:/usr/local/miniconda/miniconda3/envs/assembly-stats/bin:/usr/local/miniconda/miniconda3/envs/blobtools/bin:/usr/local/miniconda/miniconda3/envs/flye/bin:/usr/local/miniconda/miniconda3/envs/kraken2/bin:/usr/local/miniconda/miniconda3/envs/mummer/bin:/usr/local/miniconda/miniconda3/envs/nanoplot/bin:/usr/local/miniconda/miniconda3/envs/quast/bin:/usr/local/miniconda/miniconda3/envs/ragtag/bin:/usr/local/miniconda/miniconda3/envs/nanocomp/bin:/usr/local/miniconda/miniconda3/envs/racon/bin:/usr/local/miniconda/miniconda3/envs/raven-assembler/bin:/usr/local/miniconda/miniconda3/envs/medaka/bin:/usr/local/miniconda/miniconda3/envs/gatk4/bin:/usr/local/miniconda/miniconda3/envs/syri_env/bin:/usr/local/miniconda/miniconda3/envs/breakdancer/bin:/usr/local/miniconda/miniconda3/envs/kraken2/bin:/usr/local/miniconda/miniconda3/envs/blast/bin:/usr/local/miniconda:/miniconda3/envs/diamond/bin:/usr/local/miniconda/miniconda3/envs/sourmash/bin:/usr/local/miniconda/miniconda3/envs/kaiju/bin:/usr/local/miniconda/miniconda3/envs/krona/bin:/usr/local/miniconda/miniconda3/envs/spades/bin:/usr/local/miniconda/miniconda3/envs/fastqc/bin:/usr/local/miniconda/miniconda3/envs/multiqc/bin" export CON DARC="/.condarc" export LC_ALL=C %post apt update -y export DEBIAN_FRONTEND=noninteractive ln -fs /usr/share/zoneinfo/Europe/Paris /etc/localtime apt install -y tzdata dpkg-reconfigure --frontend noninteractive tzdata apt-get install -y apt-utils python3-pyqt5 pyqt5-dev-tools qttools5-dev-tools gnupg2 curl apt-get install -y unzip wget libcurl4 build-essential cmake git-all tar gzip zlib1g-dev libncurses-dev apt-get install -y minimap2 seqtk samtools bedtools vcftools bcftools assemblytics bandage # Dedicated install to ONT analyses, unpacked mkdir -p /opt/ wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | apt-key add - echo 'deb http://mirror.oxfordnanoportal.com/apt focal-stable non-free' | tee /etc/apt/sources.list.d/nanoporetech.sources.list apt-get update apt-get install -y ont-guppy-cpu ## bwa mem2 mkdir -p /opt/bwa-mem2 cd /opt/bwa-mem2 && curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2 | tar jxf - ln -s /opt/bwa-mem2/bwa-mem2-2.0pre2_x64-linux/bwa-mem2.avx2 /usr/bin/bwa-mem2 ## snpeff mkdir -p /opt/ cd /opt/ && wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip unzip /opt/snpEff_latest_core.zip ln -s /opt/snpEff/snpEff.jar /usr/bin/snpEff.jar ln -s /opt/snpEff/SnpSift.jar /usr/bin/SnpSift.jar apt-get clean mkdir /usr/local/miniconda && cd /usr/local/miniconda wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh chmod +x Miniconda3-latest-Linux-x86_64.sh ./Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda/miniconda3 && rm Miniconda3-latest-Linux-x86_64.sh cd /usr/local/miniconda/miniconda3/bin export PATH="/usr/local/miniconda/miniconda3/bin:$PATH" >> $SINGULARITY_ENVIRONMENT conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda update --all --yes conda create -n fastqc --no-default-packages conda install fastqc -n fastqc conda clean --all --yes conda create -n multiqc --no-default-packages conda install multiqc -n multiqc conda clean --all --yes conda create -n flye --no-default-packages conda install flye=2.9 -n flye conda clean --all --yes conda create -n nanocomp --no-default-packages conda install nanocomp -n nanocomp conda clean --all --yes conda create -n raven-assembler --no-default-packages conda install raven-assembler -n raven-assembler conda clean --all --yes conda create -n ragtag --no-default-packages conda install ragtag -n ragtag conda clean --all --yes conda create -n mummer --no-default-packages conda install mummer -n mummer conda clean --all --yes conda create -n racon --no-default-packages conda install racon -n racon conda clean --all --yes conda create -n assembly-stats --no-default-packages conda install assembly-stats -n assembly-stats conda clean --all --yes conda create -n nanoplot --no-default-packages conda install nanoplot -n nanoplot conda clean --all --yes conda create -n quast --no-default-packages conda install python=3.7 quast -n quast conda clean --all --yes conda create -n blobtools --no-default-packages conda install blobtools -n blobtools conda clean --all --yes conda create -n medaka --no-default-packages conda install medaka -n medaka conda clean --all --yes conda create -n gatk4 --no-default-packages conda install gatk4 -n gatk4 conda clean --all --yes conda create -n breakdancer --no-default-packages conda install breakdancer -n breakdancer conda clean --all --yes conda create -n syri_env --no-default-packages conda install syri -n syri_env conda clean --all --yes conda install -c bioconda perl-config-general perl-gd perl-math-bezier perl-math-round perl-math-vecstat perl-params-validate perl-readonly perl-set-intspan circos ### pour la metagenomique veterans burkina conda create -n kraken2 --no-default-packages conda install kraken2 -n kraken2 conda clean --all --yes conda create -n diamond --no-default-packages conda install diamond -n diamond conda clean --all --yes conda create -n blast --no-default-packages conda install blast -n blast conda clean --all --yes conda create -n sourmash --no-default-packages conda install sourmash -n sourmash conda clean --all --yes conda create -n kaiju --no-default-packages conda install kaiju -n kaiju conda clean --all --yes conda create -n spades --no-default-packages conda install spades -n spades conda clean --all --yes %runscript exec /bin/bash "$@"