03.old_create_app_03.md

layout	title	tagline
page	Create a Custom Application	Build wrapper and test scripts

If you have been following along, your fastqc app directory should contain:

fastqc/
├── Dockerfile                 # done !
├── build.sh                   # done !
├── deploy.sh
├── example                    # done !
│   ├── SP1.fq                 # done !
│   ├── SP1_fastqc.html        # done ! (can remove)
│   └── SP1_fastqc.zip         # done ! (can remove)
├── fastqc-0.11.5
│   ├── _util
│   │   └── container_exec.sh
│   ├── app.json
│   ├── app.yml
│   ├── job.json
│   ├── runner-template.sh
│   └── tester.sh
└── src                        # done !
    ├── README.md              # done !
    └── fastqc_v0.11.5.zip     # done ! (optional)

#### Write the test script

The test script allows you to test your app with real data as it will be run in production. We use shell variables liberally in the script to facilitate integration with Agave later. Edit the test script located at ~/fastqc/fastqc-0.11.5/tester.sh as follows:

#!/usr/bin/env bash

fastq="/example/SP1.fq"
example_mount="-v ${PWD}/../example:/example:rw"

CONTAINER_IMAGE="index.docker.io/USERNAME/fastqc:0.11.5"

. _util/container_exec.sh

COMMAND="perl /FastQC/fastqc"
PARAMS="${fastq}"

DEBUG=1 container_exec ${example_mount} ${CONTAINER_IMAGE} ${COMMAND} ${PARAMS}

######################
#  FUNCTIONAL TESTS  #
#                    #
# Dont include in    #
# runner-template.sh #
######################

function cleanup() {
    rm -f .container_exec.*
}

function validate_output() {
    return 0
}

function run_tests() {
    validate_output
    return 0
}

run_tests && \
    echo "Success" && \
    cleanup

The fastq variable is the only runtime variable used in this app (provided by the user through Agave). It is explicitly defined here for testing purposes, but will be removed for the purposes of the wrapper script. Similarly, the example_mount directory is also mounted to the container only for purposes of testing, but will not be mounted in production.

For the CONTAINER_IMAGE variable, replace USERNAME with your Docker ID (or project space where the image is located). Also in the above file, the container_exec.sh script is sourced, 'perl /FastQC/fastqc' is the command to execute, and the parameter passed to the command is the input fastq file (${fastq}). The final command in the script (begging with DEBUG=1) is the main container run command.

At the bottom of the script are a few template functions that you can develop to validate that the test ran correctly. Here, they are blank, and it is up to the user to write appropriate tests if desired. Test your workflow by executing:

% bash tester.sh
+ docker run --rm --user=0:20 -v /Users/username/fastqc/fastqc-0.11.5:/ home:rw -w /home -v /Users/username/fastqc/fastqc-0.11.5/../example:/ex ample:rw index.docker.io/USERNAME/fastqc:0.11.5 fastqc /example/SP1.fq
Started analysis of SP1.fq
Analysis complete for SP1.fq
+ '[' '!' -z 1 ']'
+ set +x
Success

A successful test will result in SP1_fastqc.html and SP1_fastqc.zip files generated in the ~/fastqc/example/ folder. (Make sure not to confuse old output files with new output files - check the time stamps or remove the output and run again).

#### Write the wrapper script

The file loacted at ~/fastqc/fastqc-0.11.6/runner-template.sh contains runtime instructions for your app in Agave. Essentially, it is a subset of your test script. Copy the test script to runner_template.sh and retain only the following lines:

CONTAINER_IMAGE="index.docker.io/USERNAME/fastqc:0.11.5"

. _util/container_exec.sh

COMMAND="perl /FastQC/fastqc"
PARAMS="${fastq}"

container_exec ${CONTAINER_IMAGE} ${COMMAND} ${PARAMS}

(Replace USERNAME with your Docker ID). Notice now we do not define fastq, as it will be defined later by Agave. We also do not mount our example data into the Docker container, as that will be taken care of in production.

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