Wrong `parallel` on Ubuntu by default

[lczech]

Hi @capoony,

I was just playing around a bit, and tried to run ./TestData/test.sh. However, I'm immediately getting errors from parallel:

Test if GNU parallel installed
*********************

done

Splitting Mpileup by contigs
*********************

X done
done

Max coverage percentile 0.7 calculation started
*********************

parallel: invalid option -- '-'
parallel [OPTIONS] command -- arguments
	for each argument, run command with argument, in parallel
parallel [OPTIONS] -- commands
	run specified commands in parallel
cat: 'TestResult/test/temp/cov/cutoffs/*': No such file or directory
done

PoolSNP started
*********************

parallel: invalid option -- 'k'
done

BadSites caluclation started
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parallel: invalid option -- 'k'
done

This is on Ubuntu 20.04. My guess is that the code is written for Mac, which might have more options for parallel?

Cheers
Lucas

[lczech]

Ah, solved it. Turns out that Ubuntu for whatever reason comes with a program called parallel, which is similar, but not exactly the GNU parallel implementation, see eg here... no idea why it is like that though, seems rather unfortunate.

Anyway, installing

sudo apt-get install parallel

fixes the problem. To avoid confusion for other users, I suggest to add this test:

# Check if it's GNU Parallel
if parallel --version 2>&1 | grep -q "GNU parallel"; then
  echo "GNU Parallel is installed."
else
  echo "Error: You are not using GNU Parallel!"
  exit 1
fi