Script to do convert data with Clodius in the cloud cleanly. Created by Alex Reynolds

convert_with_clodius.sh

#!/bin/bash

ENVIRONMENT=$1
ASSEMBLY=$2
RESOLUTION=$3
STATES=$4
STATESFN=$5
MARKSFN=$6
FILETOMOVESRC=$7
FILETOMOVEDEST=$8

>&2 echo "CREATE ${ENVIRONMENT}"
conda create -n ${ENVIRONMENT} python=3.6 --no-default-packages --yes

>&2 echo "ACTIVATE ${ENVIRONMENT}"
source activate ${ENVIRONMENT}

>&2 echo "INSTALL ${ENVIRONMENT}"
pip install --upgrade pip
pip install --ignore-installed scipy==1.1.0
pip install --ignore-installed numpy==1.12.0
pip install --ignore-installed h5py==2.6.0
pip install clodius==0.9.3

>&2 echo "RUN ${ENVIRONMENT}"
clodius convert bedfile-to-multivec ${MARKSFN} \
    --assembly ${ASSEMBLY} \
    --starting-resolution ${RESOLUTION} \
    --row-infos-filename ${STATESFN} \
    --num-rows ${STATES} \
    --format epilogos
mv ${FILETOMOVESRC} ${FILETOMOVEDEST}

>&2 echo "DEACTIVATE ${ENVIRONMENT}"
source deactivate ${ENVIRONMENT}

>&2 echo "REMOVE ${ENVIRONMENT}"
conda remove -n ${ENVIRONMENT} --all --yes