motroy/U50-cdc:latest

$ singularity pull shub://motroy/U50-cdc:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:latest

%environment
export PATH="/miniconda/miniconda3/:/miniconda/miniconda3/bin:/U50_tool/U50/:$PATH"
export PERL5LIB="/miniconda/miniconda3/lib:$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 openssh-server locales #build-essential zlib1g-dev libboost-all-dev
locale-gen en_US.UTF-8
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 mummer=3.23 bwa=0.7.17 samtools=1.8 bedtools=2.29.2 quast=5.0.2 python=3.6 #bowtie2=2.3.5
/miniconda/miniconda3/bin/conda install -c conda-forge biopython=1.76
export PATH="/miniconda/miniconda3/:/miniconda/miniconda3/bin:$PATH"
export PERL5LIB="/miniconda/miniconda3/lib:$PERL5LIB"

mkdir /U50_tool && cd /U50_tool
git clone https://github.com/CDCgov/U50.git
export PATH="/U50_tool/U50/:$PATH"
export LC_ALL=C

Collection

• Name: motroy/U50-cdc
• License: Apache License 2.0

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