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unipept-cli

Unipept command line interface

https://github.com/unipept/unipept-cli

Science Score: 44.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary

Keywords

metaproteomics unipept

Keywords from Contributors

bioinformatics gene-ontology-terms similarity-metric
Last synced: 7 months ago · JSON representation ·

Repository

Unipept command line interface

Basic Info
  • Host: GitHub
  • Owner: unipept
  • License: mit
  • Language: TypeScript
  • Default Branch: main
  • Homepage: http://unipept.ugent.be
  • Size: 11.8 MB
Statistics
  • Stars: 5
  • Watchers: 4
  • Forks: 2
  • Open Issues: 15
  • Releases: 29
Topics
metaproteomics unipept
Created almost 11 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

unipept-cli

NPM Version

Unipept-cli offers a command line interface to the Unipept web service. Documentation about the web service can be found at http://unipept.ugent.be/apidocs, documentation about the command line tools at http://unipept.ugent.be/clidocs.

Installation

To use the Unipept CLI, node 22 or higher needs to be installed. You can check this by running node -v on the commandline:

$ node -v v22.3.0

More information on installing Node can be found at https://nodejs.org/en/download/package-manager

The Unipept CLI is available as an npm package. This means it can easily be installed with the following command:

bash $ npm install -g unipept-cli added 3 packages in 986ms

After successful installation, the unipept command should be available:

bash $ unipept --version 4.0.0

The help can be accessed by running unipept -h.

Owner

  • Name: Unipept
  • Login: unipept
  • Kind: organization
  • Email: unipept@ugent.be
  • Location: Ghent, Belgium

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
preferred-citation:
  type: article
  authors:
  - family-names: "Verschaffelt"
    given-names: "Pieter"
  - family-names: "Van Thienen"
    given-names: "Philippe"
  - family-names: "Van Den Bossche"
    given-names: "Tim"
  - family-names: "Van der Jeugt"
    given-names: "Felix"
  - family-names: "De Tender"
    given-names: "Caroline"
  - family-names: "Martens"
    given-names: "Lennart"
  - family-names: "Dawyndt"
    given-names: "Peter"
  - family-names: "Mesuere"
    given-names: "Bart"
    orcid: "https://orcid.org/0000-0003-0610-3441"
  doi: "10.1093/bioinformatics/btaa553"
  journal: "Bioinformatics"
  start: 4220
  end: 4221
  title: "Unipept CLI 2.0: adding support for visualizations and functional annotations"
  issue: 14
  volume: 36
  year: 2020

GitHub Events

Total
  • Create event: 60
  • Issues event: 2
  • Release event: 1
  • Delete event: 51
  • Issue comment event: 18
  • Push event: 76
  • Pull request event: 110
  • Pull request review event: 43
Last Year
  • Create event: 60
  • Issues event: 2
  • Release event: 1
  • Delete event: 51
  • Issue comment event: 18
  • Push event: 76
  • Pull request event: 110
  • Pull request review event: 43

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 725
  • Total Committers: 10
  • Avg Commits per committer: 72.5
  • Development Distribution Score (DDS): 0.532
Top Committers
Name Email Commits
Toon Willems w****n@g****m 339
Bart Mesuere B****e@U****e 243
Pieter Verschaffelt p****t@u****e 53
Tom Naessens T****s@U****e 31
dependabot[bot] 4****]@u****m 29
dependabot-preview[bot] 2****]@u****m 15
Peter Dawyndt p****t@u****e 7
pcvthien p****n@g****m 4
Bart Mesuere m****t@g****m 3
pcvthien p****n@u****e 1
Committer Domains (Top 20 + Academic)
ugent.be: 5

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 13
  • Total pull requests: 214
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 24 days
  • Total issue authors: 7
  • Total pull request authors: 6
  • Average comments per issue: 1.38
  • Average comments per pull request: 0.37
  • Merged pull requests: 147
  • Bot issues: 1
  • Bot pull requests: 187
Past Year
  • Issues: 1
  • Pull requests: 106
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.25
  • Merged pull requests: 71
  • Bot issues: 1
  • Bot pull requests: 105
View more stats
Top Authors
Issue Authors
  • pverscha (4)
  • bmesuere (3)
  • pcvthien (2)
  • magnuspalmblad (1)
  • KunathBJ (1)
  • dwishsan (1)
Pull Request Authors
  • dependabot[bot] (186)
  • bmesuere (29)
  • dependabot-preview[bot] (16)
  • pverscha (7)
  • tibvdm (1)
  • pcvthien (1)
Top Labels
Issue Labels
enhancement (5) migrated (1)
Pull Request Labels
dependencies (202) javascript (54) security (4) enhancement (3) bug (1) codex (1)

Packages

  • Total packages: 2
  • Total downloads:
    • npm 2 last-month
    • rubygems 120,829 total
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 62
  • Total maintainers: 5
rubygems.org: unipept

Command line interface to the Unipept (http://unipept.ugent.be) web services (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for handling proteins using the command line.

  • Versions: 55
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 120,829 Total
Rankings
Downloads: 7.7%
Dependent packages count: 15.7%
Forks count: 16.5%
Stargazers count: 19.8%
Average: 21.3%
Dependent repos count: 46.8%
Maintainers (2)
nudded unipept
Last synced: 8 months ago
npmjs.org: unipept-cli

Command line interface to the Unipept web services

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2 Last month
Rankings
Dependent repos count: 26.0%
Average: 31.9%
Dependent packages count: 37.8%
Maintainers (3)
unipept-admin pverscha bmesuere
Last synced: 8 months ago

Dependencies

Gemfile rubygems
  • juwelier >= 0 development
  • minitest ~> 5.14 development
  • rake ~> 13.0.1 development
  • rubocop ~> 1.11 development
  • cri ~> 2.15.10
  • psych ~> 4.0.3
  • typhoeus ~> 1.3.1
Gemfile.lock rubygems
  • addressable 2.8.0
  • ast 2.4.2
  • builder 3.2.4
  • cri 2.15.11
  • descendants_tracker 0.0.4
  • ethon 0.12.0
  • faraday 1.3.0
  • faraday-net_http 1.0.1
  • ffi 1.12.1
  • git 1.11.0
  • github_api 0.19.0
  • hashie 3.6.0
  • highline 2.0.3
  • json 2.6.2
  • juwelier 2.4.9
  • jwt 2.2.2
  • kamelcase 0.0.2
  • mini_portile2 2.8.0
  • minitest 5.16.2
  • multi_json 1.15.0
  • multi_xml 0.6.0
  • multipart-post 2.1.1
  • nokogiri 1.13.6
  • oauth2 1.4.4
  • parallel 1.22.1
  • parser 3.1.2.0
  • psych 4.0.4
  • public_suffix 4.0.6
  • racc 1.6.0
  • rack 2.2.3.1
  • rainbow 3.1.1
  • rake 13.0.6
  • rchardet 1.8.0
  • rdoc 6.4.0
  • regexp_parser 2.5.0
  • rexml 3.2.5
  • rubocop 1.31.2
  • rubocop-ast 1.18.0
  • ruby-progressbar 1.11.0
  • ruby2_keywords 0.0.4
  • semver2 3.4.2
  • stringio 3.0.2
  • thread_safe 0.3.6
  • typhoeus 1.3.1
  • unicode-display_width 2.2.0
.github/workflows/ci.yml actions
  • actions/checkout v1 composite
  • ruby/setup-ruby v1 composite
unipept.gemspec rubygems