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Docker.md

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Use the Docker version

Install Docker

Please refer to Docker's manual page.

Pull the image of MiFish

docker pull taobioinfo/mifish:latest

Old versions (such as v1.0.2) are also available, though not recommended.

Run

# Get testing data from GitHub
git clone https://github.com/billzt/MiFish.git
cd MiFish/test

# run
# the first and second parameter must be in relative path starting from the current working directory
docker run --rm --workdir=/home -v $(pwd):/home docker.io/taobioinfo/mifish seq mifishdbv3.83.fa -d seq2

Limitations

  • Running speed is about four times slower than that on native Linux OS.
  • Paths of 1) amplicon sequencing data, and 2) RefDB of your metabarcoding primers, must be in relative path starting from the current working directory. That is, ./seq or ./mifishdbv3.83.fa is OK, but /home/user/data/seq/ or /home/user/data/mifishdbv3.83.fa can not be used.