POST /create-conda-env

Automatically create the conda enviroment (.yaml file) required for reproducing a computational biology paper.

Input: DOI or a PDF of a scientific paper.

Request

Content-Type: multipart/form-data

Accepted keys: doi and file

JSON Body (if using DOI):

{
  "doi": "10.1038/s41592-020-01005-z"
}

JSON Body (if uploading a PDF):

file: "path_to_file.pdf"

Note: If both a doi and a file key are present in the request, the API uses the file key by default.

Response

{
    "doi": "10.3390/ijms22031484",
    "pdf_url": null,
    "pdf_source_filename": "ijms-22-01484-v3.pdf",
    "pmcid": "PMC7867340",
    "software_tools": [
        {
            "name_in_paper": "fastqc",
            "version_in_paper": "0.11.9",
            "role_in_paper": "Data quality check",
            "access_point_raw": "[45]",
            "_matchType": "exact_light",
            "_toolInfo": {
                "conda_package": "fastqc",
                "channel": "bioconda",
                "language_hint": "Java/Perl"
            }
        },
        {
            // more tools if they exist
        }
    ],
    "conda_yaml": ".. contents of a conda env yaml file",
}