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setup.sh
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setup.sh
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#!/bin/bash
# run all tutorial scripts using slurm dependencies
cd 01_Raw_Reads
jid1=$(sbatch --parsable getdata.sh)
cd ../02_Quality_Control/
jid2=$(sbatch --parsable --dependency=afterok:$jid1 qc_raw.sh)
jid3=$(sbatch --parsable --dependency=afterok:$jid2 trimmomatic.sh)
jid4=$(sbatch --parsable --dependency=afterok:$jid3 qc_trimmed.sh)
cd ../03_Assembly/
jid5=$(sbatch --parsable --dependency=afterok:$jid4 trinity.sh)
jid6=$(sbatch --parsable --dependency=afterok:$jid5 kallisto.sh)
cd ../04_Clustering/
jid7=$(sbatch --parsable --dependency=afterok:$jid6 vsearch.sh)
cd ../05_TranscriptomeQC/
jid8=$(sbatch --parsable --dependency=afterok:$jid7 rnaQuast.sh)
jid9=$(sbatch --parsable --dependency=afterok:$jid8 busco.sh)
cd ../06_Counts/
jid10=$(sbatch --parsable --dependency=afterok:$jid9 kallisto_index.sh)
jid11=$(sbatch --parsable --dependency=afterok:$jid10 kallisto_counts.sh)
cd ../07_Coding_Regions/
jid12=$(sbatch --parsable --dependency=afterok:$jid11 01_transdecoder_longORFs.sh)
jid13=$(sbatch --parsable --dependency=afterok:$jid12 02_split_peptides.sh)
jid14=$(sbatch --parsable --dependency=afterok:$jid13 03_hmmscan.sh)
jid15=$(sbatch --parsable --dependency=afterok:$jid14 04_combine_hmmscan.sh)
jid16=$(sbatch --parsable --dependency=afterok:$jid15 05_transdecoder_predict.sh)
cd ../08_EnTAP/
jid17=$(sbatch --parsable --dependency=afterok:$jid16 entap.sh)