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aging-research
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species

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dvc.yaml 2.9 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/gestation_days
    14. 

  14.       - data/interim/selected/lifespan
    15. 

  15.       - data/interim/selected/mass_kg
    16. 

  16.       - data/interim/selected/metabolic_rate
    17. 

  17.       - data/interim/selected/mtGC
    18. 

  18.       - data/interim/selected/temperature
    19. 

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

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

  21.       - data/output/counts/species_tissue_sample_count.tsv
    22. 

  22.       - data/output/notebooks/select_samples.ipynb
    23. 

  23.   shap_selection:
    24. 

  24.     cmd: papermill -f parameters/shap_selection.yaml  --progress-bar --report-mode
    25. 

  25.       notebooks/shap_selection.ipynb data/output/notebooks/shap_selection.ipynb
    26. 

  26.     deps:
    27. 

  27.       - parameters/shap_selection.yaml
    28. 

  28.       - data/interim/selected/gestation_days
    29. 

  29.       - data/interim/selected/lifespan
    30. 

  30.       - data/interim/selected/mass_kg
    31. 

  31.       - data/interim/selected/metabolic_rate
    32. 

  32.       - data/interim/selected/mtGC
    33. 

  33.       - data/interim/selected/temperature
    34. 

  34.     outs:
    35. 

  35.       - data/output/notebooks/shap_selection.ipynb
    36. 

  36.       - data/interim/stage_1/results_concatenated.tsv
    37. 

  37.       - data/interim/stage_2/input_data
    38. 

  38.       - data/output/plots/stage_one_summary_lifespan.svg
    39. 

  39.       - data/output/plots/stage_two_untuned_summary_lifespan.svg
    40. 

  40.   tune:
    41. 

  41.     cmd: python tune.py
    42. 

  42.     params:
    43. 

  43.       - parameters/tune.yaml:
    44. 

  44.           - trait
    45. 

  45.           - metrics
    46. 

  46.           - trials
    47. 

  47.           - folds
    48. 

  48.           - hold_outs
    49. 

  49.           - repeats
    50. 

  50.           - not_validated_species
    51. 

  51.           - threads
    52. 

  52.           - debug_local
    53. 

  53.     deps:
    54. 

  54.       - data/interim/selected/gestation_days
    55. 

  55.       - data/interim/selected/lifespan
    56. 

  56.       - data/interim/selected/mass_kg
    57. 

  57.       - data/interim/selected/metabolic_rate
    58. 

  58.       - data/interim/selected/mtGC
    59. 

  59.       - data/interim/selected/temperature
    60. 

  60.   results_intersections:
    61. 

  61.     cmd: papermill -f parameters/results_intersections.yaml  --progress-bar --report-mode
    62. 

  62.       notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
    63. 

  63.     deps:
    64. 

  64.       - parameters/results_intersections.yaml
    65. 

  65.       - data/output/external/causality
    66. 

  66.       - data/output/external/linear
    67. 

  67.       - data/output/external/shap
    68. 

  68.       - data/output/external/causality/causal_relations_5_tissues_anton_species_5_bootstraps.csv
    69. 

  69.     outs:
    70. 

  70.       - data/output/notebooks/results_intersections.ipynb
    71. 

  71.       - data/output/intersections/genage_human_intersections.tsv
    72. 

  72.       - data/output/intersections/genage_model_intersections.tsv
    73. 

  73.       - data/output/intersections/intersections_5_and_7.tsv
    74. 

  74.       - data/output/intersections/intersections.tsv
    75. 

  75.       - data/output/intersections/new_old_comparison.tsv
    76.
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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

Are you sure you want to delete this access key?

No
Yes
Integrate AWS S3
Use S3 remote
Select bucket
Access key
Finish

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

Are you sure you want to delete this access key?

No
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