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aging-research
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species

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dvc.yaml 2.6 KB
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  1. stages:
    2. 

  2.   select_samples:
    3. 

  3.     cmd: papermill -f parameters/select_samples.yaml  --progress-bar --report-mode
    4. 

  4.       notebooks/select_samples.ipynb data/output/notebooks/select_samples.ipynb
    5. 

  5.     deps:
    6. 

  6.       - parameters/select_samples.yaml
    7. 

  7.       - data/input/genes/by_animal_class
    8. 

  8.       - data/input/species.tsv
    9. 

  9.       - data/input/samples.tsv
    10. 

  10.       - data/input/total_mtDNA_base_composition.csv
    11. 

  11.       - notebooks/select_samples.ipynb
    12. 

  12.     outs:
    13. 

  13.       - data/interim/selected/species.tsv
    14. 

  14.       - data/interim/selected/samples.tsv
    15. 

  15.       - data/interim/selected/genes.tsv
    16. 

  16.       - data/interim/selected/expressions.tsv
    17. 

  17.       - data/interim/selected/genes_meta.tsv
    18. 

  18.       - data/output/counts/species_sample_count.tsv
    19. 

  19.       - data/output/counts/tissue_sample_count.tsv
    20. 

  20.       - data/output/counts/species_tissue_sample_count.tsv
    21. 

  21.       - data/output/notebooks/select_samples.ipynb
    22. 

  22.   tune:
    23. 

  23.     cmd: python tune.py
    24. 

  24.     deps:
    25. 

  25.         - data/interim/selected/species.tsv
    26. 

  26.         - data/interim/selected/samples.tsv
    27. 

  27.         - data/interim/selected/genes.tsv
    28. 

  28.         - data/interim/selected/expressions.tsv
    29. 

  29.         - data/interim/selected/genes_meta.tsv
    30. 

  30.     outs:
    31. 

  31.         #- data/output/notebooks/tuning.ipynb
    32. 

  32.         - data/output/optimization/study.sqlite
    33. 

  33.     metrics:
    34. 

  34.         - data/output/optimization/parameters.json
    35. 

  35.         - data/output/optimization/metrics.tsv
    36. 

  36.   shap_selection:
    37. 

  37.     cmd: papermill -f parameters/shap_selection.yaml  --progress-bar --report-mode
    38. 

  38.       notebooks/shap_selection.ipynb data/output/notebooks/shap_selection.ipynb
    39. 

  39.     deps:
    40. 

  40.       - parameters/shap_selection.yaml
    41. 

  41.       - data/interim/selected/species.tsv
    42. 

  42.       - data/interim/selected/samples.tsv
    43. 

  43.       - data/interim/selected/genes.tsv
    44. 

  44.       - data/interim/selected/expressions.tsv
    45. 

  45.       - data/interim/selected/genes_meta.tsv
    46. 

  46.     outs:
    47. 

  47.       - data/output/notebooks/shap_selection.ipynb
    48. 

  48.   results_intersections:
    49. 

  49.     cmd: papermill -f parameters/results_intersections.yaml  --progress-bar --report-mode
    50. 

  50.       notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
    51. 

  51.     deps:
    52. 

  52.       - parameters/results_intersections.yaml
    53. 

  53.       - data/output/external/causality
    54. 

  54.       - data/output/external/linear
    55. 

  55.       - data/output/external/shap
    56. 

  56.       - data/output/external/causality/causal_relations_5_tissues_anton_species_5_bootstraps.csv
    57. 

  57.     outs:
    58. 

  58.       - data/output/notebooks/results_intersections.ipynb
    59. 

  59.       - data/output/intersections/genage_human_intersections.tsv
    60. 

  60.       - data/output/intersections/genage_model_intersections.tsv
    61. 

  61.       - data/output/intersections/intersections_5_and_7.tsv
    62. 

  62.       - data/output/intersections/intersections.tsv
    63. 

  63.       - data/output/intersections/new_old_comparison.tsv
    64.
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Integrate Google Cloud Storage
Use Google Storage
Select bucket
Upload key
Finish

Use Google Cloud Storage!

Browsing data directories saved to Google Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Google Storage bucket

Service Account Key

Congratulations!

species is now integrated with Google Cloud Storage!

Delete Storage Key

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Integrate AWS S3
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Use AWS S3 as storage!

Browsing data directories saved to S3 is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your S3 bucket

Access key (If needed)

Congratulations!

species is now integrated with AWS S3!

Delete Storage Key

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Yes
Integrate S3 compatible storage
Use S3 like remote
Select bucket
Access key
Finish

Use any S3 compatible storage!

Browsing data directories saved to S3 compatible storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your S3 bucket

Access key (If needed)

Congratulations!

species is now integrated with your S3 compatible storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes
Integrate Azure Cloud Storage
Use Azure Storage
Select bucket
Set key
Finish

Use Azure Cloud Storage!

Browsing data directories saved to Azure Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Azure Storage bucket

Access key (If needed)

Congratulations!

species is now integrated with Azure Cloud Storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes