Tool to submit genomics pipeline outputs to the ENCODE Portal

Navigation

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

Unverified details

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

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
Finally, 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

Usage

$ accession --accession-metadata metadata.json \
            --pipeline-type mirna \
            --server 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

Unverified details

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

Release history Release notifications | RSS feed

4.8.4

4.8.3

4.8.2

4.8.1

4.8.0

4.7.1

4.7.0

4.6.0

4.5.0

4.4.0

4.3.0

4.2.0

4.1.0

4.0.3

4.0.2

4.0.1

4.0.0

3.11.0

3.10.0

3.9.1

3.9.0

3.8.2

3.8.1

3.8.0

3.7.0

3.6.0

3.5.0

3.4.0

3.3.0

3.2.3

3.2.2

3.2.1

3.2.0

3.1.0

3.0.6

3.0.5

3.0.4

3.0.3

3.0.2

3.0.1

3.0.0

2.8.0

2.7.0

2.6.0

2.5.0

2.4.3

2.4.2

2.4.1

2.4.0

2.3.1

2.3.0

2.2.2

2.2.1

2.2.0

2.1.0

2.0.0

1.9.0

1.8.0

1.7.1

1.7.0

1.6.0

1.5.1

1.5.0

1.4.0

1.3.1

1.3.0

1.2.2

This version

1.2.1

1.2.0

1.1.0

1.0.1

1.0.0

0.1.0

0.0.37

0.0.36

0.0.35

0.0.34

0.0.33

0.0.32

0.0.31

0.0.30

0.0.25

0.0.24

0.0.23

0.0.22

0.0.21

0.0.20

0.0.19

0.0.18

0.0.17

0.0.16

0.0.15

0.0.14

0.0.13

0.0.12

0.0.11

0.0.10

0.0.9

0.0.8

0.0.7

0.0.6

0.0.5

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

accession-1.2.1.tar.gz (47.3 kB view details)

Uploaded Source

Built Distribution

accession-1.2.1-py3-none-any.whl (63.9 kB view details)

Uploaded Python 3

File details

Details for the file accession-1.2.1.tar.gz.

File metadata

  • Download URL: accession-1.2.1.tar.gz
  • Upload date:
  • Size: 47.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/40.6.2 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.6.10

File hashes

Hashes for accession-1.2.1.tar.gz
Algorithm Hash digest
SHA256 11c7f7fdb07d0dbf9ac07488f316ee3702520aa7e420280c71fc10e52d876573
MD5 99032a1b2097af08fd8a7f79da1f3565
BLAKE2b-256 ca7518d03b7ec67dcc64e1453097eea3576f21924db1a024d02c791a78b6f987

See more details on using hashes here.

File details

Details for the file accession-1.2.1-py3-none-any.whl.

File metadata

  • Download URL: accession-1.2.1-py3-none-any.whl
  • Upload date:
  • Size: 63.9 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/40.6.2 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.6.10

File hashes

Hashes for accession-1.2.1-py3-none-any.whl
Algorithm Hash digest
SHA256 e660b86dece4c11d7dbf86d439a981545178c8b4798d07284541f75375efaffc
MD5 38c1223cf859103bd87f1934c35e119b
BLAKE2b-256 65a0e4c9324a71d6208bf209df5a7093827052ba172dc7d15e38b20cf084f508

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page