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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/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.     params:
    25. 

  25.       - parameters/tune.yaml: #not really using this yaml file yet
    26. 

  26.         - name
    27. 

  27.         - trials
    28. 

  28.         - folds
    29. 

  29.         - hold_outs
    30. 

  30.         - threads
    31. 

  31.         - species_in_validation
    32. 

  32.         - not_validated_species
    33. 

  33.         - repeats
    34. 

  34.     deps:
    35. 

  35.         - data/interim/selected/species.tsv
    36. 

  36.         - data/interim/selected/samples.tsv
    37. 

  37.         - data/interim/selected/genes.tsv
    38. 

  38.         - data/interim/selected/expressions.tsv
    39. 

  39.         - data/interim/selected/genes_meta.tsv
    40. 

  40.     outs:
    41. 

  41.         #- data/output/notebooks/tuning.ipynb
    42. 

  42.         - data/output/optimization/study.sqlite
    43. 

  43.     metrics:
    44. 

  44.         - data/output/optimization/parameters.json
    45. 

  45.         - data/output/optimization/metrics.tsv
    46. 

  46.   shap_selection:
    47. 

  47.     cmd: papermill -f parameters/shap_selection.yaml  --progress-bar --report-mode
    48. 

  48.       notebooks/shap_selection.ipynb data/output/notebooks/shap_selection.ipynb
    49. 

  49.     deps:
    50. 

  50.       - parameters/shap_selection.yaml
    51. 

  51.       - data/interim/selected/species.tsv
    52. 

  52.       - data/interim/selected/samples.tsv
    53. 

  53.       - data/interim/selected/genes.tsv
    54. 

  54.       - data/interim/selected/expressions.tsv
    55. 

  55.       - data/interim/selected/genes_meta.tsv
    56. 

  56.     outs:
    57. 

  57.       - data/output/notebooks/shap_selection.ipynb
    58. 

  58.   results_intersections:
    59. 

  59.     cmd: papermill -f parameters/results_intersections.yaml  --progress-bar --report-mode
    60. 

  60.       notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
    61. 

  61.     deps:
    62. 

  62.       - parameters/results_intersections.yaml
    63. 

  63.       - data/output/external/causality
    64. 

  64.       - data/output/external/linear
    65. 

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

  66.       - data/output/external/causality/causal_relations_5_tissues_anton_species_5_bootstraps.csv
    67. 

  67.     outs:
    68. 

  68.       - data/output/notebooks/results_intersections.ipynb
    69. 

  69.       - data/output/intersections/genage_human_intersections.tsv
    70. 

  70.       - data/output/intersections/genage_model_intersections.tsv
    71. 

  71.       - data/output/intersections/intersections_5_and_7.tsv
    72. 

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

  73.       - data/output/intersections/new_old_comparison.tsv
    74.
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Integrate Google Cloud Storage
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Specify your Google Storage bucket

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species is now integrated with Google Cloud Storage!

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Use AWS S3 as storage!

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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?

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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