motroy/singularity-ekidna:latest

$ singularity pull shub://motroy/singularity-ekidna:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:latest

%environment
export PATH="/miniconda/miniconda3/:/miniconda/miniconda3/bin:/minimap2:/minimap2/misc:/ekidna/bin:$PATH"
export PERL5LIB="/miniconda/miniconda3/lib:$PERL5LIB"
export CONDARC=/.condarc
export LC_ALL=C

%post
#install miniconda3
export CONDARC=/.condarc
mkdir /miniconda && cd /miniconda
apt update && apt install -y git curl wget less locate build-essential openssh-server zlib1g-dev libboost-all-dev perl libmoo-perl liblist-moreutils-perl libjson-perl #python3 python3-numpy python3-scipy python3-pip
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 /miniconda/miniconda3
/miniconda/miniconda3/bin/conda config --file /.condarc --add channels defaults && /miniconda/miniconda3/bin/conda config --file /.condarc --add channels conda-forge && /miniconda/miniconda3/bin/conda config --file /.condarc --add channels bioconda
/miniconda/miniconda3/bin/conda install -c bioconda shovill abricate mlst skesa iqtree samtools bcftools seqtk bedtools snp-sites any2fasta prokka snippy gubbins
export PATH="/miniconda/miniconda3/:/miniconda/miniconda3/bin:$PATH"
export PERL5LIB="/miniconda/miniconda3/lib:$PERL5LIB"
# install minimap2
cd /
git clone https://github.com/lh3/minimap2
cd minimap2 && make
cp /minimap2/misc/paftools.js /minimap2/misc/paftools
# install the k8 javascript shell
curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
cp k8-0.2.4/k8-`uname -s` k8              # or copy it to a directory on your $PATH
export PATH="$PATH:`pwd`:`pwd`/misc"    # run this if k8, minimap2 or paftools.js not on your $PATH
cd /
git clone https://github.com/tseemann/ekidna.git
#sed -i -e 's|#!/usr/bin/env perl|#!/miniconda/miniconda3/bin/perl|g' /ekidna/bin/ekidna
export PATH="/ekidna/bin:$PATH"
abricate --setupdb
mlst --longlist
prokka --setupdb

Collection

• Name: motroy/singularity-ekidna
• License: MIT License

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