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Add apptainer conda loading instructions #655

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Add apptainer conda loading instructions
derrik-gratz May 11, 2026
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 11, 2026
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45 changes: 45 additions & 0 deletions docs/installation.md
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Expand Up @@ -203,6 +203,51 @@ Then run the following command to execute the container:
apptainer run --nv rsc.sif
```

If you encounter errors importing the package inside the container, you may need to activate the conda environment inside the container:

<details><summary>Example loading error:</summary>
```python
>>> import rapids_singlecell as rsc
Traceback (most recent call last):
File "<python-input-0>", line 1, in <module>
import rapids_singlecell as rsc
File "/src/rapids_singlecell/src/rapids_singlecell/__init__.py", line 3, in <module>
import cuml.internals.logger as logger
File "/opt/conda/lib/python3.14/site-packages/cuml/__init__.py", line 16, in <module>
import cupy
File "/opt/conda/lib/python3.14/site-packages/cupy/__init__.py", line 18, in <module>
from cupy import _core # NOQA
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.14/site-packages/cupy/_core/__init__.py", line 5, in <module>
from cupy._core import core # NOQA
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "cupy/_core/core.pyx", line 1, in init cupy._core.core
File "cupy/_core/_routines_math.pyx", line 7, in init cupy._core._routines_math
File "cupy/_core/_reduction.pyx", line 1, in init cupy._core._reduction
File "cupy/_core/_cub_reduction.pyx", line 260, in init cupy._core._cub_reduction
File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 86, in get_nvcc_path
_nvcc_path = _get_nvcc_path()
File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 198, in _get_nvcc_path
cuda_path = get_cuda_path()
File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 78, in get_cuda_path
_cuda_path = _get_cuda_path()
File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 151, in _get_cuda_path
conda_cuda_path = _get_conda_cuda_path()
File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 130, in _get_conda_cuda_path
cuda_path = os.path.join(conda_prefix, 'targets', arch)
File "<frozen posixpath>", line 77, in join
TypeError: expected str, bytes or os.PathLike object, not NoneType
>>>
```
</details>

```bash
source /opt/conda/etc/profile.d/conda.sh
conda activate base
python3
...
```


# System requirements

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