We now will explore how to use your own and public apps in your project workspace
Log into INCLUDE DataHub
In your browser navigage to https://includedcc.org/
Proceed through the following steps:
- Initial login through the INCLUDE Data Hub:
- Login with google or ORCID
Here is an example of logging in with ORCID
Your landing page is the dashboard - from there you can login to CAVATICA
In your browser navigate to "https://cavatica.sbgenomics.com"
Login here:
You are then in an environment where you can see a number of things including public and developer tabs
As in all things these days, to push or at times use (if your application is private) applications you have in the repository - you will need to authenticate with your personal authentication token. You should not share your token with others.
To use an application within your project, you need to copy that application to your project
In this example, the user navigated through the public apps looking for the FastQC analysis application and copied it to the Elements of Style project workspace.
Data are required and the same files that were used in the Nextflow workflow example were copied up onto the CAVATICA workspace.
Then the analysis was run and we can view the resulting files in the same way that you can view the results of the execution example ran on the Google Shell Cloud -- but we are in a workspace now where we can have a large number of machines running in parallel. There are limits of course, and depending upon the analysis these limits can be discussed -- because the important things is to get the Science done properly and efficiently.
You all have been invited into my project workspace so that you can have access to the items and work that we walked through today.
You can also head over and see what tasks have been run (both successful and unsuccessful)
We just illustrated how to build your single process container with Docker within the Google Shell environment.
With every container there are three steps
- Build - done with:
docker build -t my-tag .- Tag
If the image is not tagged with the appropriate name for the destination registry, you have to tag it again.
docker tag [image] [pgc-images.sbgenomics.com/deslattesmaysa2/fastqc:v1.0- Push
To be used the image needs to be in a repository.
This is how the apps were tagged here:
This bears repeating as all the work is done with the Authentication Token
Before you can do the Push step, you will also need to know how to login.
The CAVATICA platform makes it pretty easy, you have to copy the commands to allow you to authenticate with your user name and your personal authentication token
docker login pgc-images.sbgenomics.com -u deslattesmaysa2 -p [personal authentication token]In order to push your image to the repository, the repository location needs to exist.
And then create the repository location for its eventual resting place
CAVATICA makes it fairly easy to succeed in putting your own applications on their site.
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CAVATICA documentation for the Apps interface: https://docs.cavatica.org/docs/public-apps
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CAVATICA documentation for Docker Basics: http://docs.cavatica.org/docs/docker-basics