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Fixing getting dnascan_dir from paths_configs instead from args.#4

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rok:fixing_dnascan_dir
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Fixing getting dnascan_dir from paths_configs instead from args.#4
rok wants to merge 1 commit intoKHP-Informatics:masterfrom
rok:fixing_dnascan_dir

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@rok rok commented Nov 27, 2019

When running DNAscan/scripts/DNAscan.py dnascan_dir is not found in args. This gets it from paths_configs instead.

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rok commented Nov 27, 2019

Issue appears when following install instructions, using Ubuntu 18.04.3 LTS on AWS EC2 and running:

/home/ubuntu$ python3 /home/ubuntu/DNAscan/scripts/DNAscan.py -in R1_001.fastq -in2 R2_001.fastq -alsgenescanner -out /home/ubuntu/reports

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