make_config

#! /bin/bash

# Create config file to be used to create a module
 
echo "Search Biocontainers (https://biocontainers.pro/registry) or DockerHub (https://hub.docker.com/)."
echo "No need to create an account to use this tool, although there are other good reasons to sign up."
echo "Select [Packages and Containers] (Biocontainers) or [Tags] (DockerHub)."
echo "Find the version you want to install and click the [copy] icon next to the [docker pull] string for that tag/version"
echo "Note: using [latest] breaks reproducibility and so is not recommended."
echo

read -p "Enter docker pull string: " docker pull string

IFS=":"
declare -a field=($string)

image=${field[0]}
tag=${field[1]}

echo
echo "Detected the following image and tag..."
echo "Image: $image"
echo "Tag: $tag"
echo

echo "Enter the containerised command."
echo "Usually this is the same as the image name, but not always."
echo "For example, the image name for VEP is [ensembl-vep] but the command is [vep]."
echo "Pay particular attention to capitalisation."
echo "For example, the image name for QTLtools is [qtltools] but the command is [QTLtools]."
echo "Press <Enter> or <Return> to accept the default value in brackets."
echo "But check carefully first."
echo

IFS="/"
declare -a field=($image)
read -p "Command [${field[-1]}]: " command
command=${command:-${field[-1]}}

echo "This tool does not (yet) handle man paths."
echo "(And not all bioinformatics tools provide man pages anyway...)"
echo "Be kind to users by providing a link to the reference manual for this tool."
echo


read -p "Reference URL: " reference
reference=${reference:-"(reference not specified)"}
IFS=" "

config_filename=${command}_${tag}.config
touch $config_filename
echo "image=$image" >> $config_filename 
echo "tag=$tag" >> $config_filename
echo "command=$command" >> $config_filename
echo "reference=$reference" >> $config_filename
echo
echo "Created config file as $config_filename in current working directory."
echo
echo "Contents of config file:"
cat $config_filename
echo
echo "Run the following command to download the container and create a wrapper file and modulefile..."
echo "make_mod $config_filename"