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Singularity.v2.14.0
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Singularity.v2.14.0
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Bootstrap: docker
From: ubuntu:20.04
IncludeCmd: yes
%labels
MAINTAINER cschu ([email protected])
VERSION v.2.14.0
%environment
export LC_ALL=C
export PATH=$PATH:/opt/software/miniconda3/bin
%post
apt-get update
apt-get install -y apt-transport-https apt-utils software-properties-common
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
apt-get install -y wget python3-pip git
mkdir -p /opt/software
# all the conda packages won't work together.. ><;
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 bioconda 'python<3.11' bwa minimap2
git clone https://github.com/cschu/gff_quantifier.git
cd gff_quantifier
git checkout 1b7e22c968e8ee673552bebd6993621db7ce563d
/opt/software/miniconda3/bin/pip install .
# trigger trigger trigger trigger trigger trigger trigger trigger