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Updates to Docs with environment management tips #169

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Feb 10, 2022
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Updates to Docs with environment management tips #169

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Singularity management tips
jordandekraker Feb 9, 2022
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Additional instructions for environment setup
jordandekraker Feb 9, 2022
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7 changes: 7 additions & 0 deletions docs/contributing/contributing.md
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Expand Up @@ -127,3 +127,10 @@ multiple subjects in each job), 1 32core job for N subjects (e.g. 10):

hippunfold PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant \
--profile cc-slurm --group-components subj=10

## Environment management
By default, singularity stores images in your home directory. HippUnfold also stores several files similarly. If your home directory is full or otherwise inaccessible, you may want to change this with the following commands:

export SINGULARITY_CACHEDIR=/YOURDIR/.cache/singularity
export SINGULARITY_BINDPATH=/YOURDIR:/YOURDIR
export HIPPUNFOLD_CACHE_DIR=/YOURDIR/.cache/hippunfold/
7 changes: 6 additions & 1 deletion docs/getting_started/installation.md
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Expand Up @@ -73,4 +73,9 @@ Run it with maximum number of cores:
singularity run -e khanlab_hippunfold_latest.sif \
PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant -p --cores all

Note that you may need to adjust your [Singularity options](https://sylabs.io/guides/3.1/user-guide/cli/singularity_run.html) to ensure this container can read and write to yout input and output directories, repsectively.
Note that you may need to adjust your [Singularity options](https://sylabs.io/guides/3.1/user-guide/cli/singularity_run.html) to ensure this container can read and write to yout input and output directories, repsectively. For example, if your home directory is full or inaccessible, you may wish to set the following singularity parameters:

export SINGULARITY_CACHEDIR=/YOURDIR/.cache/singularity
export SINGULARITY_BINDPATH=/YOURDIR:/YOURDIR

, where `YOURDIR` is your preferred storage location.