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SpheMakh/stimela_singularity.md

Last active June 3, 2019 09:22
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Stimela with singularity
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stimela_singularity.md

You have to use singularity now. Do this:

create a folder in your home called "STIMELA_IMAGES"

mkdir $HOME/STIMELA_IMAGES

add an environment variable called "STIMELA_IMAGES_PATH" (add it at the bottom of your $HOME/.bashrc file

export STIMELA_IMAGES_PATH=$HOME/STIMELA_IMAGES
source $HOME/.bashrc

pull singularity containers

cd $STIMELA_IMAGES && stimela pull --singularity

If you are using meerkathi, then add the -sid $STIMELA_IMAGES option to your run command.

If you are running a stimela script you will need to specify the singularity_image_dir argument when you instantiate your recipe,

recipe = stimela.Recipe(..., singularity_image_dir=os.environ["STIMELA_IMAGES_PATH"])

then proceed as normal.

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