As a novice to bioinformatics, it’s very difficult for me to use qsub to complete my work

[BioOmics]

Great job! but i have some problems when i used your software

Here is your pipeline

cd umap
python ubismap.py -h
python ubismap.py \
   data/genome.fa data/chrsize.tsv \
   data/TestGenomeMappability \
   all.q --kmer 8 12 -write_script test_run.sh \
   $BOWTIEDIR/bowtie-build
sh test_run.sh

I can use your demo data to generate the test_run.sh script (by the way, although i don't understand what dose all.q mean) by ubismap.py.

But next,

How to use test_run.sh is very difficult for me to use qsub to complete my work in my server base on Ubuntu.

So, how to change the following code generated by test_run.sh to the mode without qsub command (because it's very difficult to install qsub for me, a novice to bioinformatics)

JOBID=$(qsub -q all.q -terse -N Index-Bowtie \
   -o data/TestGenomeMappability/genome/index_genome.LOG \
   -e data/TestGenomeMappability/genome/index_genome.ERR \
   -cwd -b y \
   /root/miniconda3/envs/ricenet/bin/bowtie-build \
   data/TestGenomeMappability/genome/genome.fa \
   data/TestGenomeMappability/genome/Umap_bowtie.ind)
IDPARTS=($(echo $JOBID | tr "." "\n"))
WAITID=${IDPARTS[0]}
echo "Submitted JOB ID $WAITID"

Sorry to bother you.

Best wishes.