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tien-tong merged 3 commits into from
Nov 25, 2025
Merged

Update installation.rst #309

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fdeeca2
Update installation.rst
yibeichan Jun 19, 2025
aad7b40
Update environment_hpc.yml
yibeichan Jun 19, 2025
9547f94
Apply suggestion from @mattcieslak
tien-tong Nov 25, 2025
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2 changes: 1 addition & 1 deletion docs/installation.rst
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Expand Up @@ -34,7 +34,7 @@ We have a `yaml` file on our repo for easily installing BABS and its dependencie
wget https://raw.githubusercontent.com/PennLINC/babs/refs/heads/main/environment_hpc.yml

# Install into a new environment called babs:
mamba create -f evironment_hpc.yml
mamba create -f environment_hpc.yml

# Activate the environment:
mamba activate babs
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42 changes: 23 additions & 19 deletions environment_hpc.yml
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Expand Up @@ -2,30 +2,34 @@ name: babs
channels:
- conda-forge
dependencies:
- apptainer
- python=3.11
- git
- git-annex
- pip
- apptainer
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@mattcieslak mattcieslak Jun 20, 2025

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We've found that the conda-forge apptainer doesn't work reliably on our HPC. I imagine that this would be true for other HPCs as well, since the admins set up the site's auto-mounts and other cluster-specific things

- p7zip
- python=3.11
- pip
# Core packages from conda-forge when available
- numpy
- pandas
- pyyaml>=6.0
- jinja2
- nibabel
- tqdm
- regex
# Testing packages
- pytest
- coverage
# Pip packages (mainly BABS and DataLad ecosystem)
- pip:
- babs>=0.1.0
- datalad>=0.17.2
- datalad-container>=1.1.6
- datalad-osf
- filelock>=3.8.0
- backoff
- coverage
- datalad >= 0.17.2
- datalad_container >= 1.1.6
- filelock >= 3.8.0
- jinja2
- nibabel
- niworkflows
- numpy
- pandas
- pyyaml >= 6.0
- qstat >= 0.0.5
- regex
- tqdm
- pytest
- pytest-cov==5.0.0
- pytest-env==1.1.3
- qstat>=0.0.5
- pytest-cov>=5.0.0
- pytest-env>=1.1.0
- pytest-timeout>=2.2.0
- pytest-xdist
- datalad-osf