Gen-Assoc

Tools and Web Service work Package
M-TDT tool Documentation.

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Index

• Introduction
• About Gen-Assoc
• Installation Guide line
  • By Cloning
    • Requirement
  • Using Docker Registry
• Usage
  • Following Steps

Introduction

• Many studies in Africa with recruitment in families (trio, nuclear families data)
• Study of Infectious disease (multifactorial diseases, complex traits)
• Need statistical analysis methods and tools to handle data from such studies

Family Base Design

About

We present a webservice version of the M-TDT (the multi-locus transmission disequilibrium test) tool. A tool developed to detect family-based multi-locus multi-allelic effects for qualitative or quantitative traits, extended from the original transmission disequilibrium test (TDT).

Installation

Two versions of the tool are available the CLI and the Webservice.

! This  Installation  guide is focused only on Webservice Version

We have two kind of installation process in easy step
by cloning the repos or using Docker container

Cloning

Requirements

Before Starting installation Part we should tell you the requirements to run the Application correctly. For the internal usage you need to install plink Binaries

Choose your System arichecture type !!!

- doesn'work correctly  on busybox  

And assure that you have git and Nodejs available in your system
end some point [Docker] but it's optional except if you want build a custum image
with the existant Docker file

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First copy the link and go to your terminal

$  git clone https://github.com/avalanche-org/Gen_Assoc.git

After then go to apps folder and install the requiered dependencies

$ cd  Gen_Assoc  ; cd apps 
$ npm install

Once it done you can finaly run the application

$ npm run build 

*hint :

Check the package.json file for more command to run

If you have some experience with Docker it's may be insterresting to make your onw build.
Some arguments inputs are allowed to custom your docker image during the build

In Dockerfile the Lines which have ARGS ARGUMENT=value statement can be modified during the build

+ $  docker build .   --build-arg  ARGUMENT=<_new_value_>  -t <your_tag_name>

Docker

For this section Docker only is required .

The Webservice is Avalaible on docker Registry

$ docker search  m-tdt   

From Docker hub

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You can pull Directly The Webservice app directly from the docker Registry

+ $  docker pull  jukoo/m-tdt

To launch The docker application

$  docker  run  -d  -p <localport>:<containerPort> jukoo/m-tdt  

The default port of the container is 4000 using environment variable

example:

docker run -d -p 3000:4000 jukoo/m-tdt

if you want to modify the default

docker run -d -e PORT=5000 -p 3000:5000 jukoo/m-tdt

Here you are now let's see to get your work done 🚀

COMPLETE OR INCOMPLETE BUILD PROCESS #CIBP

The docker image provided is a complete image that contains the whole application of the application available at the following address docker hub.

Here are the step to get full build of image

1 -> build the docker image using the current Dockerfile

$> docker build .  -t <yourImageTagName> 

From here we have a basic image of the application
but you have to take into account that every time you start the application it will do an installation dependencies for a first operation

To go to the complete phase of the image

you have to proceed as follows:

once the first step is over, we enter the container

$> docker run -d --name <container_name> -p<hostPort>:<containerPort> <yourImageTagName>  
$> docker exec -ti <container_name> bash    
#> cd /mTDT 

You will find a file RpkgAutorun.py (it allows to deduct the missing libraries) to install them

#> ./RpkgAutorun.py --install or -i  

(It will take some time)

Once it's finished, we leave the container

#>exit  

And we go to the last step.

We create a snapshot of the image

$> docker commit -m <message> -a <outside> <container_name> <yourImageTagName>:<version> 

this version : will be the complete version of the application, which includes dependencies.

complete and incomplete:

Incomplete Image:

-> because you have to build the dependencies
-> also count the time to build the dependencies

Complete Image : everything is already upstream

If you want to do some manipulation more it would be better to use the incomplete image
otherwise if you just want to use the application on the complete image

BASIC DOCKER IMAGE -> MTDT IMCOMPLETE IMAGE (APPLICATION) -> MTDT COMPLETE IMAGE (APPLICATION + BINARIES)

Love Pull Request