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software

Spliced Transcripts Alignment to a Reference © Alexander Dobin, 2009-2018 https://www.ncbi.nlm.nih.gov/pubmed/23104886

Software and its description is available at : https://github.com/alexdobin/STAR
software instalation @anthill23

Before you can use STAR software at anthill you need to install it.

Firstly login to anthill23.cent1.uw.edu.pl and open an interactive session :

srun -p test --pty bash -l

Then run following commands ( it will take less than 6 minutes ) :

mkdir -p ~/anthill23_soft/STAR
cd ~/anthill23_soft/STAR
wget "https://github.com/alexdobin/STAR/archive/master.zip"
unzip master.zip
cd STAR-master/source
make STAR -j ${SLURM_NTASKS}

As a result you will get STAR executable binary :

/home/users/${USER}/anthill23_soft/STAR/STAR-master/source/STAR

batch file template

First login to anthill23.cent1.uw.edu.pl.

Then create job file (batch), and save it as i.e. star_testrun.batch .

#!/bin/bash -l
#SBATCH --job-name=STAR_test
#SBATCH --partition=long
#SBATCH --ntasks=8
#SBATCH --mem 16G

#STAR binary executable path
STARBINPATH=/home/users/${USER}/anthill23_soft/STAR/STAR-master/source/
 
#printout some info
echo "STAR at anthill test"
echo "date: " `date`
echo "node_name: " `hostname`

#run STAR program with --help argument
${STARBINPATH}/STAR --help

Then run created batch file ( value 60628 is jobID, it will be different in each job submission):

[anteater@anthill23 tests]$ sbatch star_testrun.batch 
Submitted batch job 60628

Depending on availability of computing nodes your job should end in just few moments, and batch output will be located in slurm-60628.out file.