From 5e2941cc1b5aac32e64c7f82deb5a7af8ad6a903 Mon Sep 17 00:00:00 2001
From: Ben Knoll <benknoll@umn.edu>
Date: Tue, 31 Oct 2023 15:36:33 -0500
Subject: [PATCH] Update docker.md

---
 docs/docker.md | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/docs/docker.md b/docs/docker.md
index 44395093..ec8a6f8a 100644
--- a/docs/docker.md
+++ b/docs/docker.md
@@ -56,6 +56,10 @@ Done deploying all servers.
 
 Once the image has started and finished deploying the servers, make a directory called ``in`` in the original directory you created and place any documents you wish to process in that directory.
 
+```bash
+mkdir in
+```
+
 The following command will process those documents on the image:
 
 ```bash
@@ -103,7 +107,7 @@ docker rm --force b9
 Now to start up BioMedICUS using the modified deployment configuration run the following command:
 
 ```bash
-docker run -it -d -v $(pwd):/b9/ -w /b9/ --name b9 nlpieumn/biomedicus:latest --config biomedicus_deploy_config.yml
+docker run -it -d -v $(pwd):/b9/ -w /b9/ --name b9 ghcr.io/nlpie/biomedicus:latest --config biomedicus_deploy_config.yml
 ```
 
 After the services finish launching you can process documents using the modified pipeline configuration with the following command:
@@ -117,13 +121,18 @@ docker exec -it b9 b9client run --config biomedicus_default_pipeline.yml --inclu
 From the previous section you may have noticed that you can modify the deployment command by appending arguments to the ``docker run`` command. Using this method it is also possible to enable RTF processing:
 
 ```bash
-docker run -it -d -v $(pwd):/b9/ -w /b9/ --name b9 nlpieumn/biomedicus:latest --rtf
+docker run -it -d -v $(pwd):/b9/ -w /b9/ --name b9 ghcr.io/nlpie/biomedicus:latest --rtf
+```
+
+Running the RTF-to-text pipeline:
+```bash
+docker exec -it b9 b9client run-rtf-to-text in out
 ```
 
 Or even RTF processing with a custom deployment configuration:
 
 ```bash
-docker run -it -d -v $(pwd):/b9/ -w /b9/ --name b9 nlpieumn/biomedicus:latest --rtf --config biomedicus_deploy_config.yml
+docker run -it -d -v $(pwd):/b9/ -w /b9/ --name b9 ghcr.io/nlpie/biomedicus:latest --rtf --config biomedicus_deploy_config.yml
 ```
 
 To process rtf add the rtf flag to the ``docker exec`` command to run the pipeline:
@@ -143,7 +152,7 @@ docker export b9 | gzip > biomedicus-latest.tgz
 And then after transferring it to the server which has restricted internet access you can import as an image using the following command:
 
 ```bash
-zcat biomedicus-latest.tgz | docker import - nlpieumn/biomedicus:latest
+zcat biomedicus-latest.tgz | docker import - ghcr.io/nlpie/biomedicus:latest
 ```
 
 From there, the ``docker run`` command at the start of this guide will work.