ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
16 of 54 committers (29.6%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (5.0%) to scientific vocabulary

Keywords

alliance bioinformatics ga4gh genome-annotation genomics global health python reference-implementation rna server variants

Keywords from Contributors

cwl protein-structure sequence-alignment genetics

Last synced: 6 months ago · JSON representation

Repository

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Basic Info

Host: GitHub
Owner: ga4gh
License: apache-2.0
Language: Python
Default Branch: master
Homepage: http://ga4gh.org
Size: 10.1 MB

Statistics

Stars: 98
Watchers: 51
Forks: 91
Open Issues: 154
Releases: 0

Archived

Topics

alliance bioinformatics ga4gh genome-annotation genomics global health python reference-implementation rna server variants

Created over 11 years ago · Last pushed about 8 years ago

Metadata Files

Readme Contributing License

README.pypi.rst

.. image:: http://genomicsandhealth.org/files/logo_ga.png

==============================
GA4GH Reference Implementation
==============================

This is the GA4GH reference implementation.

Full documentation is available at `read-the-docs.org
`_.

- For a quick start with the GA4GH API, please see our
  `demo `_.
- To configure and deploy the GA4GH server in production
  please see the
  `installation
  `_
  page.
- If you would like to contribute to the project, please see the
  `development
  `_
  page.

Owner

Name: Global Alliance for Genomics and Health
Login: ga4gh
Kind: organization
Email: theglobalalliance@genomicsandhealth.org

Website: http://ga4gh.org
Repositories: 115
Profile: https://github.com/ga4gh

An international coalition, formed to enable the sharing of genomic and clinical data.

GitHub Events

Total

Watch event: 2

Last Year

Watch event: 2

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,057
Total Committers: 54
Avg Commits per committer: 19.574
Development Distribution Score (DDS): 0.75

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Danny Colligan	d**n@g**m	264
Jerome Kelleher	jk@w****k	201
David Steinberg	d**d@r**m	150
Brian Walsh	b**n@b**m	77
Sean Upchurch	s**u@a**u	64
Maciek Smuga-Otto	m**a@g**m	50
Gabriel Saldana	g**l@g**g	39
Irene Papakonstantinou	i**e@l**t	25
Kevin Osborn	k**2@u**u	19
Andrew Jesaitis	a**w@a**m	17
Pablo Cingolani	p**i@g**m	13
ejacox	j**n@h**m	11
Joe Zhu	s**u@g**m	9
Pat Shields	y**n@g**m	9
Isaac Ellmen	i**n@g**m	9
melaniedc	m**c@g**m	8
Molly Zhang	m**g@u**u	8
Steven G. Hershman	h**n@g**m	8
kerrydc	k**c@g**m	7
Adam Novak	a**k@s**u	6
Tom Hudson	t**n@g**m	6
cassiedoll	c****l	4
James Uther	j**s@l**t	4
Matthew Sackman	m**w@l**t	4
Pete Rolph	p**e@l**t	3
Andrew Yates	a**s@e**k	3
Audrey Musselman-Brown	m**y@g**m	2
Bettie Jea	b**a@u**u	2
Kriti Sen Sharma	k**n@p**m	2
sguthrie	s**e@g**m	2
and 24 more...

Committer Domains (Top 20 + Academic)

lshift.net: 5 ucsc.edu: 5 google.com: 3 soe.ucsc.edu: 2 sanger.ac.uk: 2 well.ox.ac.uk: 1 resium.com: 1 bwalsh.com: 1 alumni.caltech.edu: 1 gabrielsaldana.org: 1 andrewjesaitis.com: 1 ebi.ac.uk: 1 paradigm4.com: 1 caltech.edu: 1 csumb.edu: 1 tevp.net: 1 ohsu.edu: 1 alumni.stanford.edu: 1 msn.com: 1 bina.roche.com: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 88
Total pull requests: 17
Average time to close issues: 6 months
Average time to close pull requests: 18 days
Total issue authors: 17
Total pull request authors: 7
Average comments per issue: 3.14
Average comments per pull request: 2.06
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

david4096 (33)
jeromekelleher (20)
dcolligan (6)
wdesouza (6)
kozbo (4)
bwalsh (2)
rdeborj (1)
saupchurch (1)
ejacox (1)
ljdursi (1)
jhl667 (1)
adamnovak (1)
zhangb1 (1)
macieksmuga (1)
jpdna (1)

Pull Request Authors

dcolligan (7)
david4096 (4)
kozbo (2)
KevinC-wk (1)
ejacox (1)
rishidev (1)
ljdursi (1)

Top Labels

Issue Labels

enhancement (26) Documentation (22) repo manager (19) QA (18) Reads (12) bug (12) low priority (10) Infrastructure (9) Variants (7) References (7) Schemas (6) discussion (6) Variant Annotation (4) client (4) auth (3) wontfix (3) help wanted (3) Sequence Annotation (2) logging (2) question (1) blocked (1) ready (1) RNA (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 7 last-month

Total dependent packages: 0
Total dependent repositories: 2
Total versions: 1
Total maintainers: 2

pypi.org: ga4gh-server

A reference implementation of the GA4GH API

Homepage: https://github.com/ga4gh/ga4gh-server
Documentation: https://ga4gh-server.readthedocs.io/
License: Apache License 2.0
Latest release: 0.3.6
published almost 9 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 7 Last month

Rankings

Forks count: 4.7%

Stargazers count: 7.3%

Dependent packages count: 10.1%

Dependent repos count: 11.6%

Average: 15.2%

Downloads: 42.5%

Maintainers (2)

kosborn dannycolligan

Last synced: 6 months ago

Dependencies

dev-requirements.txt pypi

PyVCF ==0.6.7 development
PyYAML ==3.11 development
Sphinx ==1.4.6 development
cherrypy ==3.2.4 development
coverage * development
flake8 ==3.2.0 development
freezegun ==0.3.6 development
guppy ==0.1.10 development
mock * development
nose * development
pep8 * development
pyaml ==15.03.1 development
python-dateutil ==2.5.1 development
snakefood ==1.4 development
sphinx_rtd_theme * development
yubico-client ==1.9.1 development

docs/environment.yml pypi

RDFLib ==4.2.1
ga4gh-client ==0.6.0a10
ga4gh-common ==0.0.7
ga4gh-schemas ==0.6.0a10.post1
peewee ==2.8.5
pysam ==0.9.0
sphinx ==1.5.1
sphinx-argparse ==0.1.15

requirements.txt pypi

Beaker ==1.8.0
Flask ==0.10.1
Flask-Cors ==2.0.1
Jinja2 ==2.7.3
Mako ==1.0.4
MarkupSafe ==0.23
PyJWT ==1.4.2
RDFLib ==4.2.1
Werkzeug ==0.11.5
alabaster ==0.7.7
cffi ==1.5.2
cryptography ==1.3.1
enum34 ==1.1.2
funcsigs ==0.4
future ==0.15.2
ga4gh-client ==0.6.0a10
ga4gh-common ==0.0.7
ga4gh-schemas ==0.6.0a10.post1
humanize ==0.5.1
idna ==2.1
ipaddress ==1.0.16
itsdangerous ==0.24
lxml ==3.4.4
oic ==0.7.6
peewee ==2.8.5
protobuf ==3.1.0.post1
pyBigWig ==0.3.2
pyOpenSSL ==0.15.1
pyasn1 ==0.1.9
pycparser ==2.14
pycrypto ==2.6.1
pyjwkest ==1.0.1
pysam ==0.9.0
requests ==2.7.0
six ==1.10.0
sphinx-argparse ==0.1.15

ecosyste.ms

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Open Source Science

ga4gh-server

Science Score: 10.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.pypi.rst

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: ga4gh-server

Rankings

Maintainers (2)

Dependencies