Apptainer_manual_mode.sh

#!/bin/bash

##################################
#                                #
#   Qiime 2 Apptainer Simplifier #
#       By: Patrick Gagne        #
#        October 5, 2021         #
#                                #
##################################

sourced=0
[[ "${BASH_SOURCE[0]}" != "${0}" ]] && sourced=1

if [ $sourced -eq 0 ]
then
    echo "ERROR: This script must be sourced, not executed (source Apptainer_manual_mode.sh optionfile)"
    exit 1
fi

optionfile=$1

if [ ! $optionfile ] || [ ! -e $optionfile ] || [ ! -r $optionfile ]
then
    echo "ERROR: you must specify a valid, accessible qiime2 optionfile"
    return 2
fi

appt_command=$( grep "APPTAINER_COMMAND" $optionfile | sed 's/APPTAINER_COMMAND=//g' | sed 's/"//g' )

if [ "$appt_command" == "" ]
then
    echo "ERROR: no apptainer command found in optionfile"
    return 3
fi

shell_command=$( echo $appt_command | sed 's/exec/shell/g' )

alias qiime="$appt_command qiime"
alias appt="$appt_command"
alias apptshell="$shell_command"


# Activating bash completion 
if [ ! -d /tmp/qiime2_appt_bashcomp ]
then
    mkdir /tmp/qiime2_appt_bashcomp
fi
q2_ver=$( $appt_command qiime info | grep "QIIME 2 release" | awk -F: '{ print $2 }' | sed 's/ //g' )
$appt_command cp /opt/conda/envs/qiime2-$q2_ver/bin/tab-qiime /home/qiime2/q2cli/cache/completion.sh /tmp/qiime2_appt_bashcomp
sed -i 's/local completion_path=/#local completion_path=/g' /tmp/qiime2_appt_bashcomp/tab-qiime
line_add=$( grep -n "local completion_path" /tmp/qiime2_appt_bashcomp/tab-qiime | awk -F: '{ print $1 }' )
sed -i "$line_add i local completion_path=/tmp/qiime2_appt_bashcomp/completion.sh" /tmp/qiime2_appt_bashcomp/tab-qiime
source /tmp/qiime2_appt_bashcomp/tab-qiime

echo "Apptainer aliases ready"
echo "use 'qiime' to launch qiime commands (you can use [TAB] to complete the commands)"
echo "use 'appt' to launch other commands within the qiime2 container (ex appt biom)"
echo "use 'apptshell' to directly interact with the a container"

return 0