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singularity_SV.def
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singularity_SV.def
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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"
export CONDARC="/.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
mv snpEff /opt/
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 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 "$@"