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
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

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

This version

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

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-2.1.0.tar.gz (62.3 kB view details)

Uploaded Source

Built Distribution

accession-2.1.0-py3-none-any.whl (83.5 kB view details)

Uploaded Python 3

File details

Details for the file accession-2.1.0.tar.gz.

File metadata

  • Download URL: accession-2.1.0.tar.gz
  • Upload date:
  • Size: 62.3 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-2.1.0.tar.gz
Algorithm Hash digest
SHA256 05c4b333f11a47c9b2487c0d8a2190f466a1054807b99cf178c3c1476e87f9ba
MD5 1dac2002237ac8352e29671b307bce91
BLAKE2b-256 73f1e3fbf889dd28200457cd2f0602325cb86a589b02930480d61706c55576ba

See more details on using hashes here.

File details

Details for the file accession-2.1.0-py3-none-any.whl.

File metadata

  • Download URL: accession-2.1.0-py3-none-any.whl
  • Upload date:
  • Size: 83.5 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-2.1.0-py3-none-any.whl
Algorithm Hash digest
SHA256 b467abb00e88d3ec81927fdf74baed1796eb4681bca0479c58c03ea4d335ed0b
MD5 eb86ff051e2f524238d41f25fa0f196c
BLAKE2b-256 662a21c223734a6fe370f931302c1a7841da1cf3c9568c2ef2d4a165de98342c

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