install.sh

set -o errexit
set -o pipefail
set -o nounset
set -o xtrace
PS4='+ (${BASH_SOURCE[0]##*/} @ ${LINENO}): ${FUNCNAME[0]:+${FUNCNAME[0]}(): }'

########################## 

kernel=$(uname --kernel-name)
machine=$(uname --machine)

if [[ ${machine} != 'x86_64' || ${kernel} != 'Linux'* ]]; then
  bash utilities/error.sh "not Linux x86_64"
  exit 1
fi 

########################## 

if ! which conda; then 
  bash utilities/error.sh "please install conda"
  exit 1
fi 

# conda create --name trfermikit python=3.8 

set +o nounset
source activate trfermikit 
set -o nounset

pip install --requirement install/requirements.txt 

########################## 

mkdir --parents bin
mkdir --parents library 

root=$PWD

bash install/bedtools.sh ${root}
bash install/samtools.sh ${root}
bash install/truvari.sh ${root}
bash install/jq.sh ${root}
bash install/mosdepth.sh ${root}
bash install/htslib.sh ${root}
bash install/bcftools.sh ${root}
bash install/minimap2.sh ${root}
bash install/mysql.sh ${root}