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Updating the README and templates #501

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47792b2
dockerfile template
erinyoung Dec 5, 2022
d75b380
Create Dockerfile_mamba
erinyoung Dec 5, 2022
16607d0
Create README.md
erinyoung Dec 5, 2022
c2b4f19
Delete Dockerfile
erinyoung Dec 5, 2022
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Update and rename dockerfile-template/Dockerfile to dockerfile-templa…
erinyoung Dec 5, 2022
f370585
Update README.md
erinyoung Dec 5, 2022
cb6161d
Changing location so GH doesn't trigger
erinyoung Dec 6, 2022
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Changing location so GH doesn't trigger
erinyoung Dec 6, 2022
6731909
Changing location so GH doesn't trigger
erinyoung Dec 6, 2022
b22a5d2
Update README.md
erinyoung Dec 6, 2022
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Update README.md
erinyoung Dec 6, 2022
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Update README.md
erinyoung Dec 6, 2022
7021d8b
Update README.md
erinyoung Dec 6, 2022
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Update README.md
erinyoung Dec 6, 2022
093908c
formatting & small tweaks to main README.md
kapsakcj Jan 31, 2023
0abc505
slight tweaks to dockerfile template (ubuntu base). Added template mi…
kapsakcj Jan 31, 2023
247f9c1
clarity on main README.md mermaid diagram and fixed dockerfile template
kapsakcj Jan 31, 2023
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Added additional text
erinyoung Jul 18, 2023
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erinyoung Jul 18, 2023
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erinyoung Jul 18, 2023
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erinyoung Jul 18, 2023
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Create Dockerfile_builder
erinyoung Jul 18, 2023
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Update to jammy
erinyoung Jul 18, 2023
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Update contribute.md
erinyoung Jul 18, 2023
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Update run_containers.md
erinyoung Jul 18, 2023
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Merge branch 'master' into erin-readme-template
erinyoung Jul 18, 2023
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erinyoung Jul 18, 2023
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added python-centric Dockerfile
erinyoung Sep 6, 2023
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erinyoung Sep 7, 2023
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erinyoung Sep 7, 2023
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kapsakcj Sep 29, 2023
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Added additional text
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erinyoung authored Jul 18, 2023
commit 53d8d0383ebef566732c6c2d782663ec7d24ab26
6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# docker-builds

This repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of tools used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.
There are several community projects that create and share containers for bioinformatic tools. This repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of tools used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.

This is a community resource, built and maintined by users from varied backgrounds and expertise levels. As such, we have provided some [templates for contributing to this repository](./dockerfile-template). If **you** would like to add a Docker image or improve upon the existing images, please fork the repository, make your changes/additions, and submit a pull request. If you are having an issue with an existing image, please submit an issue. We welcome any and all feedback!

@@ -50,7 +50,7 @@ The [StaPH-B Docker User Guide](https://staphb.org/docker-builds/) was created t
docker build --tag tool:test --target test <directory to Dockerfile>
docker build --tag samtools:test --target test samtools/1.15

# Download a docker image from dockerhub (most tools have a 'latest' tag)
# Download a docker image from dockerhub (most tools have a 'latest' version tag)
docker pull staphb/tool:version
docker pull staphb/shigatyper:2.0.2

@@ -71,7 +71,7 @@ Several template files are provided. These are intended to be copied and edited

### What about Singularity?

For many people Docker is not an option, but Singularity is. Most Docker containers are compatible with Singularity and can easily be converted to Singularity format. Please see the [User Guide](https://staphb.org/docker-builds/) for instructions on how to download docker images from dockerhub and how to run them using Singularity. We've worked hard to ensure that our containers are compatibile with Singularity, but if you find one that isn't, please leave an issue and let us know!
For many people, Docker is not an option, but Singularity is. Most Docker containers are compatible with Singularity and can easily be converted to Singularity format. Please see the [User Guide](https://staphb.org/docker-builds/) for instructions on how to download docker images from dockerhub and how to run them using Singularity. We've worked hard to ensure that our containers are compatibile with Singularity, but if you find one that isn't, please leave an issue and let us know!

### Summarized usage guide for singularity