xsetup_Sc

#!/bin/bash
#

echo "Presumably you see this file because you already cloned GoSTRIPES"
echo "by the following commands (assuming for this example that you cloned"
echo "into your home directory (~):"
echo ""
echo "  cd"
echo "  git clone https://github.com/BrendelGroup/GoSTRIPES"
echo ""
echo "To set up a working directory, go to some clean directory and"
echo "execute this script, e.g."
echo ""
echo "  cd /projects/TRYgoSTRIPES"
echo "  ~/GoSTRIPES/templates/xsetup_Sc"
echo ""
echo "This will put required data from the GoSTRIPES data directory"
echo "and required repositories (including Singularity Hub) into"
echo "your current working directory."
echo ""

installdir="$( cd $( dirname "${BASH_SOURCE[0]}" )/..  && pwd )"
workingdir="$( pwd )"

mkdir ./STRIPES
cd ./STRIPES
singularity pull https://BrendelGroup.org/SingularityHub/GoSTRIPES.sif

mkdir ScGENOME
cd ScGENOME
cp ${installdir}/data/ScGENOME/0README ./
cp ${installdir}/data/ScGENOME/Sc_rRNA.fa ./
source 0README
cd ..

cp -r ${installdir}/data/downloads ./
cp ${installdir}/templates/samples.tsv ./

echo "The following will show the files that have been prepared in our"
echo "working directory:"
echo ""
pwd
ls -RC

echo ""
echo "We are ready!"
echo ""
echo 'Execute the following line, which will set up $rws as a shortcut to'
echo "run commands using the GoSTRIPES.sif apptainer:"
echo ""
echo "source ${installdir}/bin/xworkStripes -b ${workingdir} -i ${workingdir}/STRIPES/GoSTRIPES.sif"
echo ""
echo ""
echo "Indeed, now the following will show and run the demo workflow:"
echo ""
echo "${installdir}/templates/xsetup_samples"
echo "cd demo_s_mock"
echo '$rws make -n'
echo '$rws make'
echo ""
echo "After you have inspected the output, you can run in succession"
echo ""
echo "$rws make cleanup"
echo "$rws make finishup"
echo ""
echo "which cleans up your working directory. The ultimate product of our"
echo "workflow will be the mapping of the cleaned-up read pairs in the"
echo ".bam and .sam files in the alignments directory."
echo ""
echo "Note: Typically, you will have multiple samples to analyze. The file"
echo "      samples.tsv is used to record all the samples (for this demo"
echo "      there is only one sample). To run all the samples, you can run"
echo "      the following commands, in the STRIPES directory, following the"
echo "      xsetup_samples step:"
echo ""
echo "${installdir}/templates/xrun_samples"
echo "${installdir}/templates/xcleanup_samples"
echo ""
echo "This will generate all the alignment files and record the results in"
echo "file bamfiles.tsv, which can be used for input to TSRchitect (see"
echo "https://github.com/vpbrendel/TSRchitect/wiki/FAQ)."
echo ""
echo "Note: If the demo fails in your attempts, a fair possibility is that"
echo "      you did not execute the source '.. xworkStripes ..' command"
echo "      discussed above. Please do that first!"