Commit 8e0a5285 authored by Michael Hall's avatar Michael Hall
Browse files

Merge branch 'bwa_without_activate' into 'master'

Remove the unnecessary conda activate in the BWA recipe

See merge request moscardo/singularity-training-2019!1
parents d64aa65b 870aa989
Bootstrap: debootstrap
OSVersion: bionic
Include: software-properties-common
apt update
apt install -y software-properties-common
apt-add-repository universe
apt update
apt install -y wget
apt install -y wget bzip2
wget -O
bash -b -p "$HOME"/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
. ./$HOME/miniconda/bin/activate
bash -b -p /opt/miniconda
export PATH="/opt/miniconda/bin:$PATH"
echo "PATH=/opt/miniconda/bin:$PATH" >> "$SINGULARITY_ENVIRONMENT"
conda install -y -c bioconda bwa
export PATH="$HOME/miniconda/bin:$PATH"
export PATH="/opt/miniconda/bin:$PATH"
command -v conda >/dev/null 2>&1 || exit 1
command -v bwa >/dev/null 2>&1 || exit 1
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