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Now that you've done everything the hard way, let's see how to do run an alignment pipeline using Anna's script.
First the setup:
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mkdir -p $SCRATCH/core_ngs/align2/fastq cd $SCRATCH/core_ngs/align2/fastq cp /corral-repl/utexas/BioITeam/core_ngs_tools/alignment/*fastq.gz . |
Before executing the script you need to have one environment variable set. We'll do it at the command line here, but you could put it in your .bashrc file.
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export path_code=/work/01063/abattenh/seq/code |
Now change into the directory and call the script with no arguments to see usage
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cd $SCRATCH/core_ngs/align2 /work/01063/abattenh/seq/$path_code/script/align/align_bwa_illumina.sh |
Run the pipeline
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/work/01063/abattenh/seq/$path_code/script/align/align_bwa_illumina.sh ./fastq/Sample_Yeast_L005_R1.cat.fastq.gz yeast_chip sacCer3 1 50 |