Commit 5bf3930d authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
Browse files

test

parent b42244b0
#!/bin/bash
## This script takes one input: the path to the HiFibr output file
## Example usage on test data: sh run_pipeline.sh test_data/polyA1Seq/PolyA1Seq_testdata.csv
if [ "$#" -ne 1 ]; then
echo "Error: please supply the path to the HiFibr input file as a command line argument"
fi
......@@ -23,10 +25,10 @@ hifi_reclass=${results_dir}/${bn}_reclassified.csv
deletion_out=${results_dir}/${bn}_deletion.txt
insertion_out=${results_dir}/${bn}_insertion.txt
source /anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate sdmmej
cd ~/Documents/git/sdmmej
#source /anaconda3/etc/profile.d/conda.sh
#conda deactivate
#conda activate sdmmej
#cd ~/Documents/git/sdmmej
echo "------"
echo "Starting to process HiFibr output file"
......
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