Tool to submit genomics pipeline outputs to the ENCODE Portal

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  • License: MIT License (MIT)
  • Author: Paul Sud
  • Requires: Python >=3.6
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Project description

Code Style: Black License: MIT CircleCI status

accession is a Python module and command line tool for submitting genomics pipeline analysis output files and metadata to the ENCODE Portal.

Installation

Note: intallation requires Python >= 3.6

$ pip install accession

Next, provide your API keys from the ENCODE portal:

$ export DCC_API_KEY=XXXXXXXX
$ export DCC_SECRET_KEY=yyyyyyyyyyy

You will also need to authenticate with Google Cloud if using WDL metadata from pipeline runs on Google Cloud. Run the following two commands and follow the prompts:

$ gcloud auth login --no-launch-browser
$ gcloud auth application-default login --no-launch-browser
In addition, it is highly recommended to set the DCC_LAB and DCC_AWARD environment variables for ease of use. These correspond to the lab and award identifiers given by the ENCODE portal, e.g. /labs/foo/ and U00HG123456, respectively.
$ export DCC_LAB=XXXXXXXX
$ export DCC_AWARD=yyyyyyyyyyy
If you would like to be able to pass Caper workflow IDs or labels you will need to configure access to the Caper server. If you are invoking accession from a machine where you already have a Caper set up, and you have the Caper configuration file available at ~/.caper/default.conf, then there is no extra setup required. If the Caper server is on another machine, you will need so configure HTTP access to it by setting the hostname and port values in the Caper conf file.
(Optional) Finally, to enable using Cloud Tasks to upload files from Google Cloud Storage to AWS S3, set the following two environment variables. If one or more of them is not set, then files will be uploaded using the same machine that the accessioning code is run from. For more information on how to set up Cloud Tasks and the upload service, see the docs for the gcs-s3-transfer-service
$ export ACCESSION_CLOUD_TASKS_QUEUE_NAME=my-queue
$ export ACCESSION_CLOUD_TASKS_QUEUE_REGION=us-west1

Usage

$ accession -m metadata.json \
            -p mirna \
            -s dev

Please see the docs for greater detail on these input parameters.

Project Information

accession is released under the MIT license, documentation lives in readthedocs, code is hosted on github and the releases on PyPI.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for paulsud from gravatar.com paulsud Avatar for perna from gravatar.com perna Avatar for ulugbek from gravatar.com ulugbek

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These details have not been verified by PyPI
Project links
Meta
  • License: MIT License (MIT)
  • Author: Paul Sud
  • Requires: Python >=3.6
Classifiers

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