From 17abf1e9cdd6b29e42fc294e70c1630427de81ef Mon Sep 17 00:00:00 2001 From: Tim Wang Date: Tue, 6 Sep 2022 10:57:55 -0400 Subject: [PATCH 1/2] Add troubleshooting note to docker directory readme file --- dockers/README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/dockers/README.md b/dockers/README.md index 9d58315e78..792493283e 100644 --- a/dockers/README.md +++ b/dockers/README.md @@ -236,4 +236,10 @@ ENTRYPOINT [ "/sbin/tini", "--" ] ## Troubleshooting +The file structure and tools in each image can be explored by instructing it to run a `bash` shell: + +```bash +docker run -it --rm bash +``` + If you have any questions or would like some more guidance on writing Dockerfiles please file a [GitHub issue in WARP](https://github.com/broadinstitute/warp/issues/new). From 1afa864a7ec9d6b07edbec4fd80f6ded3658e630 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Tue, 6 Sep 2022 11:43:34 -0400 Subject: [PATCH 2/2] Update README.md --- dockers/README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dockers/README.md b/dockers/README.md index 792493283e..e8c9ed7da0 100644 --- a/dockers/README.md +++ b/dockers/README.md @@ -16,7 +16,7 @@ This style guide provides formatting guidelines and best practices for writing D * [Proper process reaping](#process) * [Build Scripts and README](#build) * [Formatting](#formatting) -* [Troubleshooting](#trouble) +* [Troubleshooting and running standalone](#trouble) ## Overview WARP maintains a collection of docker images which are used as execution environments for various cloud-optimized data processing pipelines. Many of these image require specific sets of tools and dependencies to run and can be thought of as _custom_ images rather than traditional application images. @@ -234,9 +234,9 @@ RUN set -eux; \ ENTRYPOINT [ "/sbin/tini", "--" ] ``` -## Troubleshooting +## Troubleshooting and running standalone -The file structure and tools in each image can be explored by instructing it to run a `bash` shell: +The WARP dockers are designed to be run from their respective WDL pipelines. However, if you need to run a Docker independent of a WDL for testing or troubleshooting, you'll likely need to explicity instruct it to run a `bash` shell in the `run` command. An example of this is shown in the terminal command below: ```bash docker run -it --rm bash