#! /bin/bash

# Script to install a tutorial to a running Galaxy instance # # usage: install_tutorial.sh </path/to/tutorial> <galaxy_url> <admin_api_keyoexample.org # # example: sh bin/install_tutorial.sh topics/metagenomics/tutorials/mothur-miseq-sop localhost:8080 admin # # make sure you have ephemeris installed: # pip install ephemeris -U #

tutorial=$1 galaxy_url=$2 api_key=$3

# install workflows and tools echo “Installing workflows” if [ -d ${tutorial}/workflows ] then

echo " - Extracting tools from workflows"
for w in ${tutorial}/workflows/*.ga
do
    workflow-to-tools -w $w -o ${tutorial}/workflows/wftools.yaml -l $(basename ${tutorial})
    echo " - Installing tools from workflow $(basename $w)" 
    shed-tools install -g ${galaxy_url} -a ${api_key} -t ${tutorial}/workflows/wftools.yaml
    rm ${tutorial}/workflows/wftools.yaml
done
echo " - Installing workflows"
workflow-install --publish_workflows -g ${galaxy_url} -a ${api_key} -w ${tutorial}/workflows/

else

echo "No workflows to install (no directory named workflow present)"

fi

# install data libraries echo “Populating Data Libraries” if [ -f ${tutorial}/data-library.yaml ] then

setup-data-libraries -g ${galaxy_url} -a ${api_key} -i ${tutorial}/data-library.yaml

else

echo "No data library to install (no file named data-libraries.yaml present)"

fi

# install reference data echo “Installing reference data” if [ -f ${tutorial}/data-manager.yaml ] then

run-data-managers -g ${galaxy_url} -a ${api_key} --config ${tutorial}/data-manager.yaml

else

echo "No reference data to install (no file named data-manager.yaml present)"

fi

# install tours –> not possible via API yet