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HubLot merged 1 commit into from
Oct 31, 2024
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complete docker image installation and usage #2

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5 changes: 5 additions & 0 deletions README.md
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Expand Up @@ -64,6 +64,11 @@ Also, docker images are built and provided through the Container registry of Git

Docker images are built only when tags or Release are created.

Pull the Docker Image:

docker pull ghcr.io/lbt-cnrs/biospring:latest

Please read [User Manual](doc/User_Manual.md) for detailed usage of the docker image.

### Compilation

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12 changes: 10 additions & 2 deletions doc/User_Manual.md
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Expand Up @@ -91,11 +91,15 @@ Example of `.msp` file for BioSpring:

After generating model.nc file and setting simulation parameters model.msp and you can launch BioSpring using this command:

biospring -s model.nc -c model.msp
biospring -s model.nc -c model.msp

Be carefull that you have set constraints and output parameters to get results. Indeed, without constraints, there is no reason that the spring
network comes out the initial equilibriumn, and without output parameters, you won't be able to get any results.

Or run the Docker image:

docker run --init -v ./:/data ghcr.io/lbt-cnrs/biospring \
biospring -s /data/model.nc -c /data/model.msp

### with interaction via VMD using MDDriver

Expand All @@ -109,8 +113,12 @@ We advice you to try BioSpring with MDDriver and VMD to understand how this inte

To run BioSpring with VMD and MDDriver, start by launching the BioSpring tools with these MDDriver parameters.

biospring -c model.nc -s model.msp --wait 1 --port 3000 --log model.log
biospring -c model.nc -s model.msp --wait --port 3000 --log model.log

Or run the Docker image:

docker run -p 3000:3000 --init -v ./:/data ghcr.io/lbt-cnrs/biospring \
biospring -s /data/model.nc -c /data/model.msp --wait --port 3000

#### Lauching VMD
Start the VMD program (double click on its icon or launch from the command line).
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