hisat2-docker

Build a Container for bioconda hisat2 For using this module with the rmats-nf workflow -- we also need to install Samtools

Steps to build this docker container.

1. Look up on anaconda the tool you wish to install
2. create an environment.yml file either manually or automatically
3. Use the template Dockerfile modifying if necessary (in our case we have no custom files for the src directory so we do not use that)
4. Build the Docker Image
5. Set up GitHub Actions

Installing Samtools

Latest version now is samtools 1.17 We will add Samtools now to this container.

To build your image from the command line:

• Can do this on Google shell - docker is installed and available

docker build -t hisat2 .

To test this tool from the command line

Set up an environment variable capturing your current command line:

PWD=$(pwd)

Then mount and use your current directory and call the tool now encapsulated within the environment.

docker run -it -v $PWD:$PWD -w $PWD hisat2 hisat2 -h

Also since we have now built samtools v1.17 in this package we can test that this tool is now available and accessible in the image

docker run -it -v $PWD:$PWD -w $PWD hisat2 samtools view -h

should return the help information for the samtools view tool.

Final word: Adding this code to your GitHub Repository

This repository was built in place and then uploaded to the repository on GitHub.

To do so in the https://shell.google.com environment we need to get install the interactive set of tools for GitHub obtainable from https://anaconda.org and with:

conda install -c conda-forge gh -y

Now we need to authenticate

gh auth login

Authenticate with your Personal Authentication Token

gh auth login
? What account do you want to log into? GitHub.com
? What is your preferred protocol for Git operations? HTTPS
? Authenticate Git with your GitHub credentials? Yes
? How would you like to authenticate GitHub CLI?  [Use arrows to move, type to filter]
  Login with a web browser
> Paste an authentication token

Now we can from the command line create this repository.

Let's go ahead and tell git who we are.

git config --global user.email "adeslat@scitechcon.org"
git config --global user.name "adeslatt"

Following GitHub's updated instructions on how to create a new repository from the command line

We now type

git init -b main

Which will return

Initialized empty Git repository in /home/adeslat/hisat2_index-docker/.git/

And then we type

git add . && git commit -m "initial commit"

which returns something like this.

[main (root-commit) d1e421f] initial commit
 3 files changed, 33 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 README.md
 create mode 100644 environment.yml

We then use the gh repo create command to create the reposistory.

gh repo create

Which then prompts us to what we need to do -- important is that what we want to do is Push an existing local repository to GitHub. The tool's remainder defaults are acceptable, because we staged ourselves with the name of the directory.

$ gh repo create
? What would you like to do? Push an existing local repository to GitHub
? Path to local repository .
? Repository name hisat2_index-docker
? Description
? Visibility Public
✓ Created repository adeslatt/fastqc-docker on GitHub
? Add a remote? Yes
? What should the new remote be called? origin
✓ Added remote https://github.com/adeslatt/hisat2_index-docker.git
? Would you like to push commits from the current branch to "origin"? Yes
✓ Pushed commits to https://github.com/adeslatt/hisat2_index-docker.git