https://github.com/stevekm/singularity-samtools-demo
Singularity container for samtools
https://github.com/stevekm/singularity-samtools-demo
singularity singularity-container
Last synced: 3 months ago
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Singularity container for samtools
- Host: GitHub
- URL: https://github.com/stevekm/singularity-samtools-demo
- Owner: stevekm
- Created: 2017-12-06T22:37:45.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2018-02-01T22:03:18.000Z (about 8 years ago)
- Last Synced: 2025-07-10T18:22:26.719Z (10 months ago)
- Topics: singularity, singularity-container
- Language: Makefile
- Homepage:
- Size: 2.24 MB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Setup
This assumes you are building a Singularity container locally on a Mac
Make sure you've already installed Vagrant, since its needed to run Singularity on a Mac
```
brew cask install virtualbox
brew cask install vagrant
brew cask install vagrant-manager
```
If you have trouble install Vagrant with homebrew, try using [this](https://releases.hashicorp.com/vagrant/2.0.1/vagrant_2.0.1_x86_64.dmg).
# Creating the Container
The workflow for creating a Singularity container on a Mac through Vagrant is saved in the included `Makefile`.
Make the container by running:
```bash
make container
```
And run a test on the created container with
```bash
make test
```
## Output
If everything worked, the following files should be created:
- `singularity-vm/image/singularity-container-samtools`: the Singularity container file for samtools
- `singularity-vm/image/samtools-version.txt`: the output from running samtools inside the container, should look like this:
```
samtools 1.6
Using htslib 1.6
Copyright (C) 2017 Genome Research Ltd.
```
# Resources
http://singularity.lbl.gov/install-mac
https://app.vagrantup.com/singularityware/boxes/singularity-2.4
https://releases.hashicorp.com/vagrant/2.0.1/vagrant_2.0.1_x86_64.dmg
http://singularity.lbl.gov/docs-build-container
http://singularity.lbl.gov/docs-recipes
https://github.com/qbicsoftware/qbic-singularity-samtools