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Copy file name to clipboardExpand all lines: build/README.md
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## build_all.py script
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This script initializes all docker containers, builds all datasets, validates them, and uploads them to figshare and pypi.
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This script initializes all docker containers, builds all datasets, validates them, and uploads them to figshare.
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It requires the following authorization tokens to be set in the local environment depending on the use case:
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`SYNAPSE_AUTH_TOKEN`: Required for beataml and mpnst datasets. Join the [CoderData team](https://www.synapse.org/#!Team:3503472) on Synapse and generate an access token.
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`PYPI_TOKEN`: This token is required to upload to PyPI.
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`FIGSHARE_TOKEN`: This token is required to upload to Figshare.
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`GITHUB_TOKEN`: This token is required to upload to GitHub.
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-`--omics`: Processes and builds the omics data files.
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-`--drugs`: Processes and builds the drug data files.
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-`--exp`: Processes and builds the experiment data files.
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-`--all`: Executes all available processes above (docker, samples, omics, drugs, exp). This does not run the validate, figshare, or pypi commands.
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-`--all`: Executes all available processes above (docker, samples, omics, drugs, exp). This does not run the validateor figshare commands.
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-`--validate`: Validates the generated datasets using the schema check scripts. This is automatically included if data upload occurs.
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-`--figshare`: Uploads the datasets to Figshare. FIGSHARE_TOKEN must be set in local environment.
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-`--pypi`: Uploads the package to PyPI. PYPI_TOKEN must be set in local environment.
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-`--high_mem`: Utilizes high memory mode for concurrent data processing. This has been successfully tested using 32 or more vCPUs.
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-`--dataset`: Specifies the datasets to process (default='broad_sanger,hcmi,beataml,mpnst,cptac').
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-`--version`: Specifies the version number for the PyPI package and Figshare upload title (e.g., "0.1.29"). This is required for figshare and PyPI upload steps. This must be a higher version than previously published versions.
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-`--version`: Specifies the version number for the Figshare upload title (e.g., "0.1.29"). This must be a higher version than previously published versions.
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-`--github-username`: GitHub username matching the GITHUB_TOKEN. Required to push the new Tag to the GitHub Repository.
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-`--github-email`: GitHub email matching the GITHUB_TOKEN. Required to push the new Tag to the GitHub Repository.
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**Example usage**:
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- Build all datasets and upload to Figshare and PyPI and GitHub.
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Required tokens for the following command: `SYNAPSE_AUTH_TOKEN`, `PYPI_TOKEN`, `FIGSHARE_TOKEN`, `GITHUB_TOKEN`.
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- Build all datasets and upload to Figshare and GitHub.
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Required tokens for the following command: `SYNAPSE_AUTH_TOKEN`, `FIGSHARE_TOKEN`, `GITHUB_TOKEN`.
parser.add_argument('--docker',dest='docker',default=False,action='store_true', help="Build all docker images.")
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parser.add_argument('--samples',dest='samples',default=False,action='store_true', help="Build all sample files.")
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parser.add_argument('--omics',dest='omics',default=False,action='store_true', help="Build all omics files.")
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parser.add_argument('--drugs',dest='drugs',default=False,action='store_true', help="Build all drug files")
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parser.add_argument('--exp',dest='exp',default=False,action='store_true', help="Build all experiment file.")
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parser.add_argument('--validate', action='store_true', help="Run schema checker on all local files. Note this will be run, whether specified or not, if figshare or pypi arguments are included.")
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parser.add_argument('--validate', action='store_true', help="Run schema checker on all local files. Note this will be run, whether specified or not, if figshare arguments are included.")
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parser.add_argument('--figshare', action='store_true', help="Upload all local data to Figshare. FIGSHARE_TOKEN must be set in local environment.")
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parser.add_argument('--pypi', action='store_true', help="Update PYPI Package with latest Figshare data. PYPI_TOKEN must be set in local environment.")
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parser.add_argument('--all',dest='all',default=False,action='store_true', help="Run all data build commands. This includes docker, samples, omics, drugs, exp arguments. This does not run the validate, figshare, or pypi commands.")
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parser.add_argument('--all',dest='all',default=False,action='store_true', help="Run all data build commands. This includes docker, samples, omics, drugs, exp arguments. This does not run the validate or figshare commands")
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parser.add_argument('--high_mem',dest='high_mem',default=False,action='store_true',help="If you have 32 or more CPUs, this option is recommended. It will run many code portions in parallel. If you don't have enough memory, this will cause a run failure.")
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parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,mpnst,mpnstpdx',help='Datasets to process. Defaults to all available.')
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parser.add_argument('--version', type=str, required=False, help='Version number for the PyPI package and Figshare upload title (e.g., "0.1.29"). This is required for Figshare and PyPI upload. This must be a higher version than previously published versions.')
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parser.add_argument('--version', type=str, required=False, help='Version number for the Figshare upload title (e.g., "0.1.29"). This is required for Figshare upload. This must be a higher version than previously published versions.')
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parser.add_argument('--github-username', type=str, required=False, help='GitHub username for the repository.')
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parser.add_argument('--github-email', type=str, required=False, help='GitHub email for the repository.')
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