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website

UseGalaxy.EU website (compiled version https://github.com/usegalaxy-eu/usegalaxy-eu.github.io)

https://github.com/usegalaxy-eu/website

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

UseGalaxy.EU website (compiled version https://github.com/usegalaxy-eu/usegalaxy-eu.github.io)

Basic Info
Statistics
  • Stars: 21
  • Watchers: 15
  • Forks: 118
  • Open Issues: 37
  • Releases: 0
Created about 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

UseGalaxy.eu Page

Fancy Redirects

Much content was moved around (in the output site) recently. That is because we're doing a strange and cool hybrid-site approach.

Page | Use ---------- | --- / | main galaxy instance /about/ | About our galaxy instance /freiburg/ | About the freiburg team /news/ | news posts /events/ | events posts

We'll be doing some fancy proxying to accomplish this. The above mentioned pages (other than /) will have the full "chrome", i.e. top bar with about/people/pubs links.

Within the main panel we'll be showing an iframe to usegalaxy.github.io/gxhome/ which will NOT be accessible via usegalaxy.eu/gxhome/.

This is a terrible explanation but basically:

  • the site should be fully functional at usegalaxy-eu.github.io. This site can be referenced in communication materials.
  • certain important subpages (/freiburg/, /news/, /events/) will be available from usegalaxy.eu/.../ in order to tie those to our galaxy instance more closely.

Server Maintenance

If you need to register a notice event, edit _data/notices.yml. When the event is over, you should comment out that file.

Duplication

You will notice there is some duplication in the templates:

Parent | Duplicate --------------- | -------------- _layout/event.html | _layout/event-galaxy.html _layout/event_list.html | _layout/event_list-galaxy.html _layout/news.html | _layout/news-galaxy.html _layout/news_list.html | _layout/news_list-galaxy.html _layout/news.md | _layout/gxnews.md _layout/events.md | _layout/gxevents.md _layout/default.md | _layout/default-galaxy.md _includes/home_news_events.html | _includes/home_news_events-galaxy.html

This duplication is intentional, it is part of the collections configuration and allows us to produce "two" sites from one set of source documents. This is done intentionally in order to allow authors to add posts once, and then on the code side we generate both a "normal" site with the full header, and a "galaxy" version without the header since a duplicate header looks quite strange in Galaxy.

If you need to edit templates, I would recommend editing the parent / normal template and then vimdiffing (or other tool of your choice) to compare that with its -galaxy.html sibling. Most of the templates will be identical except for the template they are inheriting from. The only major differences is that the normal templates read for post in site.posts (or site.events) while the galaxy templates read for post in site.posts_plain (or site.events_plain)

Adding Posts

These are used for tool notices / other server notices. Run:

bundle exec jekyll post "My new post"

The only required metadata are tags and title, you should remove layout as that is inherited / specified automatically. If you put tools in the tags a wrench icon will show with the post.

Adding Events

You will need to manually create an event in the folder _events. The metadata for events is a bit more complex, it looks like:

```yaml

tags: title: Software Carpentry workshop starts: 2017-03-09 ends: 2017-03-10 organiser: name: Freiburg Galaxy Team email: galaxy@informatik.uni-freiburg.de location: Georges-Köhler-Allee, Freiburg im Breisgau, Germany ```

Here we specify an starts and ends to define the dates of the event. Providing an organiser name and email is recommended to allow people to contact you easily regarding the event.

Supplying a location is used in the user's calendar (if it supports it). E.g. when the user adds the event to their google calendar, they will see a map of the location and can easily get directions to it.

Labels for Posts and Events

  • article
  • Bioconda
  • citations
  • conda-forge
  • conference
  • COVID-19
  • data
  • devops
  • FAQ
  • galaxy
  • GCC
  • grants
  • hackathon
  • hardware
  • jobs
  • MMOS
  • newsletter
  • paper
  • papercuts
  • PGP
  • poster
  • release
  • report
  • society
  • streetscience
  • support
  • s4f
  • talk
  • TIaaS
  • tools
  • training
  • video

Adding new member sites

If you contribute substantially to this service, we invite you to become a "member site"! A member site is one of our ways to say "thank you" and acknowledge your contribution. You can add events to get more exposure, you can add your funding agencies, own blog posts and present your team and publications. To add your side please see this example pull- request.

Building

This website is jekyll based and can be build as every other jekyll page.

If you have conda around and no jekyll setup, we do provide a Makefile that sets up and conda environment, with all what you need.

console make install make run

Deploying

Our Jenkins bot deploy the website using

console make install make build and the script .deploy.sh.

Owner

  • Name: useGalaxy.eu
  • Login: usegalaxy-eu
  • Kind: organization
  • Email: contact@galaxyproject.eu
  • Location: Europe

Citation (citations.md) 

---
layout: default
---

# Scientific research using & citing the European Galaxy server

<br>
This is the list of scientific publications that cited the European Galaxy instance sorted by year.
Please help us to support this project with your [acknowledgement](/about).
<br><br>

{% bibliography --file citations-eu --file citations-eu-manual %}

## Patents

{% bibliography --file citations-eu --file citations-eu-manual -q @patent[year>1900] %}

GitHub Events

Total
  • Issues event: 4
  • Watch event: 2
  • Delete event: 46
  • Issue comment event: 23
  • Push event: 189
  • Pull request review comment event: 10
  • Pull request review event: 58
  • Pull request event: 179
  • Fork event: 1
  • Create event: 49
Last Year
  • Issues event: 4
  • Watch event: 2
  • Delete event: 46
  • Issue comment event: 23
  • Push event: 189
  • Pull request review comment event: 10
  • Pull request review event: 58
  • Pull request event: 179
  • Fork event: 1
  • Create event: 49

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 5
  • Total pull requests: 190
  • Average time to close issues: over 1 year
  • Average time to close pull requests: about 1 month
  • Total issue authors: 5
  • Total pull request authors: 29
  • Average comments per issue: 0.8
  • Average comments per pull request: 0.17
  • Merged pull requests: 151
  • Bot issues: 1
  • Bot pull requests: 139
Past Year
  • Issues: 3
  • Pull requests: 96
  • Average time to close issues: about 4 hours
  • Average time to close pull requests: 1 day
  • Issue authors: 3
  • Pull request authors: 14
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.15
  • Merged pull requests: 70
  • Bot issues: 1
  • Bot pull requests: 75
View more stats
Top Authors
Issue Authors
  • igormakunin2 (1)
  • github-actions[bot] (1)
  • NickSto (1)
  • gmauro (1)
  • anilthanki (1)
Pull Request Authors
  • github-actions[bot] (137)
  • wm75 (9)
  • bgruening (4)
  • bebatut (4)
  • dadrasarmin (3)
  • Deeptivarshney (2)
  • Sch-Da (2)
  • sanjaysrikakulam (2)
  • nilchia (2)
  • dependabot[bot] (2)
  • SaimMomin12 (2)
  • pavanvidem (2)
  • itisAliRH (2)
  • dianichj (2)
  • dsavchenko (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2) good first issue (1)

Dependencies

.github/workflows/optimize-images.yml actions
  • actions/checkout v2 composite
  • calibreapp/image-actions main composite
  • peter-evans/create-pull-request v3 composite
.github/workflows/update-citations.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • peter-evans/create-pull-request v3 composite
.github/workflows/update-genome-count.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • peter-evans/create-pull-request v3 composite
.github/workflows/update-tools.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • peter-evans/create-pull-request v3 composite
Gemfile.lock rubygems
  • addressable 2.7.0
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  • jekyll-compose >= 0 development
  • jekyll-feed ~> 0.6 development
  • bibtex-ruby >= 5.1.0
  • html-proofer >= 0
  • jekyll >= 4
  • jekyll-scholar >= 0
  • jekyll-twitter-plugin >= 0
  • nokogiri >= 1.10.8
  • tzinfo-data >= 0
environment.yml conda
  • bibtexparser
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  • gdbm 1.18.*
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  • gxx_linux-64 13.1.0.*
  • icu 64.2.*
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  • pyzotero
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requirements.txt pypi
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