Update with astrocyte_cli

README.md

 # Astrocyte Container Images
 
-A skeleton repo acting as a host registry for various images used in Astrocyte.
+A skeleton repo acting as a host registry for various images used in Astrocyte.
\ No newline at end of file
+
+## Astrocyte_cli
+The astrocyte_cli container includes Astrocyte 2.0.0 (under development), Nextflow 22.04.5, Singularity 3.9.8 and Python 3.7.13. It can be used as tool to check and test the Astrocyte workflows during development.
+
+### Reqirements
+It requires the usner namespace UID/GID mapping to use the interal Singularity.
+
+https://docs.sylabs.io/guides/3.5/admin-guide/user_namespace.html
+
+### Usage
+
+* Load the Singularity module on BioHPC Cluster/Workstation
+```
+module load singularity/3.5.3
+```
+
+* Pull the Astrocyte CLI image
+```
+singularity -v pull docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte-container-images/astrocyte_cli:2.0.0
+```
+
+* Run the image to see the help info. It is suggested to use the `run` command to run the image instead of the `exec` command
+```
+singularity run astrocyte_cli_2.0.0.sif -h
+```
+
+* Clone the Astrocyte word count example and checkout to the right version
+```
+git clone https://git.biohpc.swmed.edu/biohpc/astrocyte_example_wordcount.git
+cd astrocyte_example_wordcount
+git checkout test_2.0.0
+```
+
+* Validate the configuration of the Astrocyte workflow
+```
+singularity run astrocyte_cli_2.0.0.sif check astrocyte_example_wordcount/
+```
+
+* Test run the Astrocyte workflow on the local host
+```
+singularity run astrocyte_cli_2.0.0.sif test astrocyte_example_wordcount/
+```
+
+* Prepare for the shiny libraries
+```
+singularity run astrocyte_cli_2.0.0.sif shiny-prepare astrocyte_example_wordcount/ --with-container
+```
+
+* Run shiny on the local host
+```
+singularity run astrocyte_cli_2.0.0.sif shiny astrocyte_example_wordcount/ --with-container
+```

astrocyte_cli/build_and_push.sh

@@ -11,6 +11,10 @@ DOCKER_PASSWORD="AA4KRFCeEg8XSmwyoaAN"
 export DOCKER_BUILDKIT=0
 export COMPOSE_DOCKER_CLI_BUILD=0
 
+#
+# Please note that the build of astrocyte_cli container requires to clone and fetch the repo manualy!
+#
+
 # build with proxy settings
 docker build --no-cache -f ./${VERSION}/Dockerfile -t ${CONTAINER_TAG} ./${VERSION}