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 >=3.5
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

$ pip install accession

In addition to installing the module, make sure to provide your API keys from the ENCODE portal:

$ export DCC_API_KEY=XXXXXXXX
$ export DCC_SECRET_KEY=yyyyyyyyyyy

You will also need Google Application Credentials in your environment. Obtain and set your service account credentials:

$ export GOOGLE_APPLICATION_CREDENTIALS=<path_to_service_account_file>
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 \
            --accession-steps steps.json \
            --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 >=3.5
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

1.2.1

1.2.0

1.1.0

1.0.1

1.0.0

0.1.0

This version

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-0.0.37.tar.gz (25.0 kB view details)

Uploaded Source

Built Distributions

accession-0.0.37-py3.6.egg (79.4 kB view details)

Uploaded Source

accession-0.0.37-py3-none-any.whl (32.2 kB view details)

Uploaded Python 3

File details

Details for the file accession-0.0.37.tar.gz.

File metadata

  • Download URL: accession-0.0.37.tar.gz
  • Upload date:
  • Size: 25.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.13.0 pkginfo/1.4.2 requests/2.21.0 setuptools/40.8.0 requests-toolbelt/0.9.1 tqdm/4.33.0 CPython/3.6.8

File hashes

Hashes for accession-0.0.37.tar.gz
Algorithm Hash digest
SHA256 a8ed6fcc5719f1d1bc692a4f7a7e0f1a03998655c354ee4a2335a362b55602bf
MD5 b95e60fb08de3d69e8a81ffbd17750a9
BLAKE2b-256 1efda9b9109b3faed587dd7175b6fe67208f6a4f1b8fbd00989961ae16ad5a82

See more details on using hashes here.

File details

Details for the file accession-0.0.37-py3.6.egg.

File metadata

  • Download URL: accession-0.0.37-py3.6.egg
  • Upload date:
  • Size: 79.4 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-0.0.37-py3.6.egg
Algorithm Hash digest
SHA256 1ce769b9bd53302281e0d0dfa7d3564e710810fa8fe3e0d78878d7ff9d1edfa3
MD5 8a45c804ce315c12f2f26cfea44edaa5
BLAKE2b-256 0725a969a63c96587de1d749a33d23d3c85e5b59a3c0aef9e7480c058ec9dbf7

See more details on using hashes here.

File details

Details for the file accession-0.0.37-py3-none-any.whl.

File metadata

  • Download URL: accession-0.0.37-py3-none-any.whl
  • Upload date:
  • Size: 32.2 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.13.0 pkginfo/1.4.2 requests/2.21.0 setuptools/40.8.0 requests-toolbelt/0.9.1 tqdm/4.33.0 CPython/3.6.8

File hashes

Hashes for accession-0.0.37-py3-none-any.whl
Algorithm Hash digest
SHA256 506491765cee455d1aeaa26aac156d721a03029112125d5ffbb28a6304a1344f
MD5 a09f29145444f34ff542a40e368edb2b
BLAKE2b-256 209130d8b2423ebfab82ccc1aa14728c8aa46f4f1a0eac6e3dbba532753edb45

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