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GoSTRIPES HOWTO - an example for how to use the software

Preparation

Fortunately, almost nothing is required! More or less, all you need to do is to pick a directory where you want to install GoSTRIPES and another directory in which you want to work. We'll assume for this demo that you want to install GoSTRIPES in your home directory and that you will be working in a directory called /scratch/TRYgoSTRIPES:

cd
git clone https://github.com/BrendelGroup/GoSTRIPES
cd /scratch/TRYgoSTRIPES

Now run the xsetup_Sc script from the templates directory, and you'll be good to go:

~/GoSTRIPES/templates/xsetup_Sc

The script will display progress and instructions, so please be sure to read the text. Importantly, the script will ask you to execute something like the following in your shell (just copy/paste what the script shows):

source ~/GoSTRIPES/bin/xworkStripes -b /scratch/TRYgoSTRIPES -i /scratch/TRYgoSTRIPES/STRIPES/gostripes.sif

This command will set up the variable rws. In our example,

echo $rws

should return

singularity exec -B /scratch/TRYgoSTRIPES /scratch/TRYgoSTRIPES/STRIPES/gostripes.sif

Executing the workflow

Unless something odd happened, you should now be able to review and run the demo as follows:

cd STRIPES
~/GoSTRIPES/templates/xsetup_samples
cd demo_s_mock
$rws make -n
$rws make

$rws <command> will execute any <command> within the GoSTRIPES container. In our workflow, make will invoke the provided Makefile, which takes care of everything else. Because all required programs and scripts are bundled in the container, there is nothing else for you to do in terms of installation.

Note: Typically, you will have multiple samples to analyze. The file samples.tsv is used to record all the samples (for this demo there is only one sample). To run all the samples, you can run the following commands, in the STRIPES directory, following the xsetup_samples step:

${installdir}/templates/xrun_samples
${installdir}/templates/xcleanup_samples

This will generate all the alignment files and record the results in file bamfiles.tsv, which can be used for input to TSRchitect (see https://github.com/vpbrendel/TSRchitect/wiki/FAQ).

Note: If the demo fails in your attempts, a fair possibility is that you did not execute the source '.. xworkStripes ..' command discussed above. Please do that first!