Lxd Pirus TestUnitaire pipeline

This pipeline do almost nothing, it's used by Pirus unit tests to test the lxd container manager. And it's a very simple pipeline that is use for tutorials

This document explain you how to build it.

Requirement

• You need LCX and LXD installed on your computer.

Automatic build instructions

git clone https://github.com/REGOVAR-Pipelines/LxdPirus_TestUnitaire.git
make build_lxc_image

If the make instruction run without error, it will create the pirus pipeline image : LxdPirus_TestUnitaire.tar.xz

You can then use it on your server to run TU (have a look to the Pirus/pirus/tests/core/test_core_lxdmanager.py to set the path where is the image).

Manual build Instructions

# create a container
lxc launch images:ubuntu/xenial pirus
# go inside the freshly created container
lxc exec pirus -- /bin/bash

# following directories are mandatory
mkdir -p /pipeline/{job,inputs,outputs,logs,db}

# need curl if you want to notify server with the progress of your run
apt install curl jq nano --fix-missing

# Create the script run.sh. this will be the "entry point" of your run
# An example can be found on github (https://github.com/REGOVAR/Pirus/blob/master/examples/pipelines/PirusBasic/run.sh)
nano /pipeline/job/run.sh
chmod +x /pipeline/job/run.sh

# To allow users to configure your pipeline, you shall put in your container a form.json file
# that will describe a form to set parameter for your pipe.
# An example can be found on github (https://github.com/REGOVAR/Pirus/blob/master/examples/pipelines/PirusBasic/form.json)
nano /pipeline/form.json

# You can also put a a custom logo (png or jpeg file) in your pipeline.

# exit the container
exit

# stop it and create an image
lxc stop pirus
lxc publish pirus --alias=PirusTest

# Your Pipeline is ready to use on your server

Export image as file and edit image conf to create a piruse package installable on any pirus server

lxc image export PirusTest
# following command shall be done as root to avoid image corruption
# (as it will try to create symlink to computer resource in /dev folder by example)
sudo tar xf <the_name_of_lxc_export_something_like_a8d44d24fcs...8fzef54e5>.tar.gz

# add folowing informations into the metadata.yaml file
sudo nano metadata.yaml

# if json
"pirus":
{
    "name" : "Pirus Test",               # required : the name of your pipe
    "description" : "Test pipeline",       # optional : the purpose of your pipe
    "version": "1.0.0",                    # optional : the version of your pipe
    "pirus_api": "1.0.0",                  # optional : the pirus api version
    "license" : "AGPLv3",                  # optional : the license of your pipe
    "developers" : ["Olivier GUEUDELOT"],  # optional : a list of name
    "job" : "/pipeline/job/run.sh",        # required : the command command that shall be execute to run your pipe (use absolute path)
    "inputs" : "/pipeline/inputs",         # optional : absolute path to the folder (in the container) where inputs files for the pipe shall be put
    "outputs" : "/pipeline/outputs",       # optional : absolute path to the folder (in the container) where ouputs files of the pipe will be put
    "databases" : "/pipeline/db",          # optional : absolute path to the folder (in the container) where tierce databases (hg19 by example) shall be put
    "logs" : "/pipeline/logs",             # optional : absolute path to the folder (in the container) where log of the run will be put
    "form" : "/pipeline/form.json",        # optional : absolute path to the json file that describe the form for the user to configure the run of the pipe
    "icon" : "/pipeline/logo.png"          # optional : absolute path to the image that shall be used as logo for the pipe
}
# if yaml
pirus:
    name: "Pirus Test"  # required
    description: "Test pipeline for pirus"
    version : "1.0.0"
    pirus_api: "1.0.0"
    license: "AGPLv3"
    developers: ["Olivier GUEUDELOT"]
    job: "/pipeline/job/run.sh"  # required
    logs: "/pipeline/logs"
    inputs: "/pipeline/inputs"
    outputs: "/pipeline/outputs"
    databases: "/pipeline/db"
    form: "/pipeline/form.json"
    icon: "/pipeline/logo.png"


# You can repackage the image in tar.xz, to save space
sudo tar cfJ PirusTest.tar.xz metadata.yaml rootfs templates
sudo rm -fr metadata.yaml rootfs templates
sudo chown olivier:olivier PirusTest.tar.xz