• This contains all of the commands to execute all components of the PTF-Persona application.
• This is a collection of applications that serve as client, server, and local executor, all wrapped up into this shell command.
• Uses the PTF-System repository to assemble PTF applications.

• All of the system runs in Docker for ease.
• If you want to build outside of Docker, replicate the steps in the Dockerfiles manually.

• Download the PTF system repository linked above
• Use the [[https://github.com/epfl-dcsl/ptf-system/blob/master/build_container.sh][build container script]] to build the PTF system packaged with the correct name.
• Further steps will be built on top of the PTF system package with this name.
• If you want to build PTF Persona outside of the Docker container, you can copy the pip wheel file out of the container. See the PTF System repo for further instructions.

• The offline conversion steps for creating an AGD dataset must be done in a prior iteration of the Persona application shell.
• This prior iteration uses the same underlying Persona library as this system (PTF-Persona), but an older version of applcation conversion.
• We will use Docker for this step for compatibility. Please replicate these steps (or similar) outside of Docker if you want a native install / build.

First, make sure that you have the code imported as a submodule to this repository by using the git command.

git submodule update --init

• Build the Docker container that contains the Persona application.
• This can be skipped if you volume-mount the current directory, but this approach keeps things cleaner.
• This docker command must be executed in the original_persona directory.

docker build --tag ptf-orig .

docker run --rm -it -v "/path/to/fastq_dataset":/dataset ptf-orig bash

• You can exercise other options for parallelism, chunking (the –chunk option) and the name. See the help option for import_fastq.

# run this in the docker container!
./persona import_fastq --chunk 100000 --name MyFirstAGD --out /dataset/MyFirstAGD.agd /dataset/my_dataset.fastq

• Now your dataset is in /path/to/fastq_dataset/MyFirstAGD.agd

• We will run this in the Docker container for this shell.
• To build this natively, consult the Docker file for the steps for building this.

• Requires the PTF System container to be available.

docker build --tag ptf-shell .

• Using the AGD dataset we made in the previous step, we map this location into the docker container and start a normal bash shell.
• You will also need to map in a location of the table that SNAP aligner uses. See their quickstart guide for how to do this. We will only need a single-end index for this example.

docker run --rm -it -v "/path/to/fastq_dataset/MyFirstAGD.agd":/agd_dataset -v "/path/to/index":/snap_index ptf-shell bash

./persona local align-sort -d /agd_dataset --fused-index-path /snap_index /agd_dataset/MyFirstAGD.json

• This research paper on Arxiv describes the architectural components of PTF that are crucial to its scale-out and multi-request capabilities.