Docker.md

Setting up and testing AmpliCI:

1. Install Docker Desktop, which includes a command line tool that we'll use below (only do this once): Docker Desktop
2. Go to the Windows command line.
3. Install the AmpliCI docker image (only do this once): docker pull kdorman/amplici:latest
4. Start an AmpliCI container (only do this once): docker run -it kdorman/amplici /bin/sh
5. Verify the software is available, read the help: run_AmpliCI --help
6. You can also try the tutorial commands as I have provided a test file (assuming you are in directory data):

   run_AmpliCI --fastq sim3.8.1.fastq --outfile error.out --error
   run_AmpliCI --fastq sim3.8.1.fastq --outfile test --abundance 2 --profile error.out
   run_AmpliCI --fastq sim3.8.1.fastq --outfile test.id --profile error.out --haplotypes test.fa

7. To stop the container: exit
8. Note the name of the container (last column): docker container ls -a

To try it out on data, the process would be generally as follows. I will type NAME instead of the name of the container you discovered in step 8 above.

Running AmpliCI on your data:

1. Go to the Windows command line
2. Copy data to the container (assuming your data are on the C disk in directory MyDataDir): docker cp c:\MyDataDir\MyData.fastq NAME:/data
3. Start the container: docker start -a -i NAME
4. In the container (you should see the prompt change to / #), go to where you copied the data: cd data
5. Run AmpliCI commands (see the README.md), producing output file I'll call AMPLICI_OUTPUT.
6. When you are done: exit
7. Copy the results files to your Windows machine: docker cp NAME:/data/AMPLICI_OUTPUT c:\MyDataDir