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docs: how to add to ccbrpipeliner module
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kelly-sovacool committed Oct 16, 2023
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Expand Up @@ -14,10 +14,28 @@ cd /data/CCBR_Pipeliner/Pipelines/CRUISE/cruise-dev
git pull
# optionally switch to different branch if needed

# install the version to a hidden path (e.g. .dev, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRUISE
# install the version to a hidden path (e.g. .v0.1.0, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRUISE
cd ..
pip install ./cruise-dev -t ./.dev
pip install ./cruise-dev -t ./.v0.1.0
# add it to your PATH and PYTHONPATH with:
export PATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.dev/bin/"
export PYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.dev/"
export PATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/bin/"
export PYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/"
```

## Add CRUISE to the ccbrpipeliner module on biowulf

Create a lua file in `/data/CCBR_Pipeliner/modules/ccbrpipeliner`, e.g. `dev.lua`.
You can copy the most recent lua file to use as a base, then modify the following line:

```lua
source_sh("bash", "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/cruise-dev/bin/install.sh .v0.1.0")
```

Change the version of CRUISE as needed. Notice the dot (`.`) in front of the version number to indicate a hidden path.

Then use and load the module (substitute `dev` for whatever you named the new lua file) with:

```sh
module use /data/CCBR_Pipeliner/modules
module load ccbrpipeliner/dev
```

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