From 8f6905559d5450c846d15c13d90774b083c0367e Mon Sep 17 00:00:00 2001 From: Anisha Keshavan Date: Tue, 5 Sep 2017 11:40:57 -0700 Subject: [PATCH 1/2] updated readme with new docker instructions --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 991281c..d9150bf 100644 --- a/README.md +++ b/README.md @@ -27,12 +27,14 @@ To pull the docker image from Docker Hub, do docker pull bids/mindboggle ``` -To run the docker, do +To run the docker, do: ``` - docker run -ti -v /path/to/bids_dir:/root/data bids/mindboggle /root/input /root/output/ participant +docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data/derivatives/ participant ``` +Its important to mount to a directory in `/home/jovyan/` because you are not root in this Docker image. + To use bash: ``` From 355677fc2a215772e741c7f437dfe9308c2751f8 Mon Sep 17 00:00:00 2001 From: Anisha Keshavan Date: Tue, 5 Sep 2017 11:41:44 -0700 Subject: [PATCH 2/2] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d9150bf..3c76705 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ Its important to mount to a directory in `/home/jovyan/` because you are not roo To use bash: ``` - docker run -ti -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/root/data --entrypoint /bin/bash bids/mindboggle + docker run -ti -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/home/jovyan/work/data --entrypoint /bin/bash bids/mindboggle ``` For developers, you can make changes to the Dockerfile, and build the docker image, by running