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Maintenance/update readme (#211)
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* fix readme aws link

* fix example recipe paths

* add v2 recipe

* add v2 one sphere recipe in readme
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rugeli authored Nov 9, 2023
1 parent 2c5e04b commit c5e731c
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Showing 2 changed files with 6 additions and 3 deletions.
5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -15,8 +15,9 @@ algorithm to pack molecular recipes
3. `pip install -e .[dev]`

### Run pack code
1. example pack recipe : `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c packing-configs/run.json`
2. example pack from remote : `pack -r github:recipes/NM_Analysis_FigureB1.0.json -c packing-configs/run.json`
1. example pack v1 recipe : `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json`
2. example pack v2 recipe : `pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/run.json`
3. example pack from remote : `pack -r github:recipes/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json`

### Run conversion code
* To convert to simularium and view at https://staging.simularium.allencell.org/viewer
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4 changes: 3 additions & 1 deletion cellpack/autopack/upy/simularium/simularium_helper.py
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Expand Up @@ -1392,7 +1392,9 @@ def post_and_open_file(self, file_name, open_results_in_browser=True):
try:
url = simulariumHelper.store_results_to_s3(simularium_file)
except Exception as e:
aws_readme_url = "https://github.com/mesoscope/cellpack/blob/feature/main/README.md#aws-s3"
aws_readme_url = (
"https://github.com/mesoscope/cellpack/blob/main/README.md#aws-s3"
)
if isinstance(e, NoCredentialsError):
print(
f"need to configure your aws account, find instructions here: {aws_readme_url}"
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