Dockerfile and image for running HybPiper with Python 3.

Pull the most recent build:

docker pull joelnitta/hybpiper

Launch the container:

docker run --rm -it joelnitta/hybpiper

You should now be inside the container, in the /home directory.

All HybPiper scripts have been added to $PATH, so you can call them directly from any directory.

Check that all dependencies are installed:

reads_first.py --check-depend

Run the HybPiper tutorial:

cd /apps/HybPiper/test_dataset
tar -zxvf test_reads.fastq.tar.gz
reads_first.py -b test_targets.fasta -r NZ281_R*_test.fastq --prefix NZ281 --bwa

...

Alternatively, you can run HybPiper commands directly from the command line by mounting a volume.

For example, mount /working/dir containing test_targets.fasta, NZ281_R1_test.fastq, and NZ281_R2_test.fastq from the tutorial data, and run reads_first.py:

docker run --rm --entrypoint reads_first.py -v /working/dir:/home joelnitta/hybpiper -b test_targets.fasta -r NZ281_R*_test.fastq --prefix NZ281 --bwa

To run a different HybPiper script, change the script name after --entrypoint and provide arguments to that script after joelnitta/hybpiper. Note that any filename arguments must have their paths relative to the working directory.