Skip to content

Commit c229fb0

Browse files
scorreardgithub-actions[bot]
scorreard
authored and
github-actions[bot]
committed
workflow4metabolomics community resources update
1 parent 44768bd commit c229fb0

19 files changed

Lines changed: 7345 additions & 6274 deletions

‎communities/workflow4metabolomics/lab/README.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
# Community subdomain/Lab

‎communities/workflow4metabolomics/lab/conclusion.html‎

Lines changed: 53 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,53 @@
1+
{% load markdown %}
2+
3+
<!-- <section class="my-5">
4+
{% if help_links %}
5+
<h4 class="mb-3">{{ lab_name }} community support</h4>
6+
<ul>
7+
{% for link in help_links %}
8+
<li>
9+
<a href="{{ link.url }}" target="_blank">{{ link.title }}</a>
10+
</li>
11+
{% endfor %}
12+
</ul>
13+
{% endif %}
14+
</section>
15+
16+
<section>
17+
<h4 class="mb-3">News and Events</h4>
18+
19+
<div class="row justify-content-center">
20+
<div class="col">
21+
<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/topics/microbiome/feed.w.xml"></iframe>
22+
</div>
23+
<div class="col">
24+
<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/microbiome-month.w.xml"></iframe>
25+
</div>
26+
</div>
27+
</section> -->
28+
29+
{% if feedback_email %}
30+
<section class="my-5">
31+
<h4 class="my-3">What do you think of the {{ lab_name }}?</h4>
32+
<button
33+
class="ga-btn"
34+
data-bs-toggle="modal"
35+
data-bs-target="#feedbackModal"
36+
>
37+
Give feedback
38+
</button>
39+
</section>
40+
{% endif %}
41+
42+
<section class="my-5">
43+
<h4 class="mb-3">Cite Us</h4>
44+
</section>
45+
46+
<section class="my-5">
47+
If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage.
48+
<!-- If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>-->
49+
</section>
50+
51+
<section id="conclusionExtra">
52+
{{ conclusion_extra_md|safe }}
53+
</section>

‎communities/workflow4metabolomics/lab/intro.html‎

Lines changed: 41 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,41 @@
1+
<section class="my-5" id="tagline">
2+
<p>
3+
Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community!
4+
</p>
5+
6+
<p>
7+
#Here include an intro to your page, see the ex mple below from the microgalaxy community
8+
# Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>. </p>
9+
<p>
10+
<a
11+
href="#"
12+
data-bs-toggle="modal"
13+
data-bs-target="#infoModal">
14+
How does this page relate to Galaxy {{ site_name }}?
15+
</a>
16+
</p>
17+
18+
{{ intro_extra_md }}
19+
20+
<div class="modal fade" id="infoModal" tabindex="-1">
21+
<div class="modal-dialog modal-lg">
22+
<div class="modal-content">
23+
<div class="modal-header">
24+
<h5 class="modal-title">Galaxy {{ site_name }}</h5>
25+
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
26+
</div>
27+
<div class="modal-body">
28+
<p>
29+
This site <em>{{ subdomain }}.{{ root_domain }}</em> is connected to the same server as <em>{{ root_domain }}</em>, but with an interface dedicated to helping our {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website.
30+
</p>
31+
<p><a class="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
32+
<p><a class="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p>
33+
<p><a class="ga-btn" href="{{support}}">Galaxy {{ site_name }} support</a></p>
34+
</div>
35+
<div class="modal-footer">
36+
<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
37+
</div>
38+
</div>
39+
</div>
40+
</div>
41+
</section>

‎communities/workflow4metabolomics/lab/sections/2_tools.yml‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
id: tools
2+
title: Community curated tools
3+
tabs: []

‎communities/workflow4metabolomics/lab/sections/3_workflows.yml‎

Lines changed: 297 additions & 0 deletions
Large diffs are not rendered by default.

‎communities/workflow4metabolomics/lab/sections/4_tutorials.yml‎

Lines changed: 153 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,153 @@
1+
id: tutorials
2+
title: Community curated tutorials
3+
tabs:
4+
- id: fair_data
5+
title: FAIR Data
6+
heading_md: 'Top 10 most visited tutorials for the Topic : FAIR Data'
7+
content:
8+
- title_md: "DataPLANT ARCs\n (Visitors: 1784805)"
9+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
10+
on the Galaxy Training Network and covering topics related to nan
11+
button_link:
12+
https://training.galaxyproject.org//topics/fair/tutorials/dataplant-arcs/tutorial.html
13+
button_tip: View tutorial
14+
button_icon: tutorial
15+
- title_md: "FAIR in a nutshell\n (Visitors: 1092)"
16+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
17+
on the Galaxy Training Network and covering topics related to nan
18+
button_link:
19+
https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html
20+
button_tip: View tutorial
21+
button_icon: tutorial
22+
- title_md: "FAIR data management solutions\n (Visitors: 479)"
23+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
24+
on the Galaxy Training Network and covering topics related to nan
25+
button_link:
26+
https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html
27+
button_tip: View tutorial
28+
button_icon: tutorial
29+
- title_md: "Making clinical datasets FAIR\n (Visitors: 438)"
30+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
31+
on the Galaxy Training Network and covering topics related to nan
32+
button_link:
33+
https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html
34+
button_tip: View tutorial
35+
button_icon: tutorial
36+
- title_md: "FAIRification of an RNAseq dataset\n (Visitors: 386)"
37+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
38+
on the Galaxy Training Network and covering topics related to nan
39+
button_link:
40+
https://training.galaxyproject.org//topics/fair/tutorials/fair-rna/tutorial.html
41+
button_tip: View tutorial
42+
button_icon: tutorial
43+
- title_md: "Persistent Identifiers\n (Visitors: 371)"
44+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
45+
on the Galaxy Training Network and covering topics related to nan
46+
button_link:
47+
https://training.galaxyproject.org//topics/fair/tutorials/fair-persistent-identifiers/tutorial.html
48+
button_tip: View tutorial
49+
button_icon: tutorial
50+
- title_md: "Exporting Workflow Run RO-Crates from Galaxy\n (Visitors: 366)"
51+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
52+
on the Galaxy Training Network and covering topics related to nan
53+
button_link:
54+
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html
55+
button_tip: View tutorial
56+
button_icon: tutorial
57+
- title_md: "Metadata\n (Visitors: 318)"
58+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
59+
on the Galaxy Training Network and covering topics related to nan
60+
button_link:
61+
https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html
62+
button_tip: View tutorial
63+
button_icon: tutorial
64+
- title_md: "FAIR and its Origins\n (Visitors: 228)"
65+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
66+
on the Galaxy Training Network and covering topics related to nan
67+
button_link:
68+
https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html
69+
button_tip: View tutorial
70+
button_icon: tutorial
71+
- title_md: "FAIR Galaxy Training Material\n (Visitors: 226)"
72+
description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
73+
on the Galaxy Training Network and covering topics related to nan
74+
button_link:
75+
https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html
76+
button_tip: View tutorial
77+
button_icon: tutorial
78+
- id: using_galaxy_and_managing_your_data
79+
title: Using Galaxy and Managing your Data
80+
heading_md: 'Top 10 most visited tutorials for the Topic : Using Galaxy and Managing
81+
your Data'
82+
content:
83+
- title_md: "Using dataset collections\n (Visitors: 17355)"
84+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
85+
on the Galaxy Training Network and covering topics related to nan
86+
button_link:
87+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html
88+
button_tip: View tutorial
89+
button_icon: tutorial
90+
- title_md: "Creating, Editing and Importing Galaxy Workflows\n (Visitors: 6536)"
91+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
92+
on the Galaxy Training Network and covering topics related to nan
93+
button_link:
94+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-editor/tutorial.html
95+
button_tip: View tutorial
96+
button_icon: tutorial
97+
- title_md: "Rule Based Uploader\n (Visitors: 5970)"
98+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
99+
on the Galaxy Training Network and covering topics related to nan
100+
button_link:
101+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html
102+
button_tip: View tutorial
103+
button_icon: tutorial
104+
- title_md: "Extracting Workflows from Histories\n (Visitors: 3249)"
105+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
106+
on the Galaxy Training Network and covering topics related to nan
107+
button_link:
108+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html
109+
button_tip: View tutorial
110+
button_icon: tutorial
111+
- title_md: "Automating Galaxy workflows using the command line\n (Visitors: 3243)"
112+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
113+
on the Galaxy Training Network and covering topics related to nan
114+
button_link:
115+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html
116+
button_tip: View tutorial
117+
button_icon: tutorial
118+
- title_md: "Using Workflow Parameters\n (Visitors: 2156)"
119+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
120+
on the Galaxy Training Network and covering topics related to nan
121+
button_link:
122+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html
123+
button_tip: View tutorial
124+
button_icon: tutorial
125+
- title_md: "Workflow Reports\n (Visitors: 1016)"
126+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
127+
on the Galaxy Training Network and covering topics related to nan
128+
button_link:
129+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html
130+
button_tip: View tutorial
131+
button_icon: tutorial
132+
- title_md: "Rule Based Uploader: Advanced\n (Visitors: 926)"
133+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
134+
on the Galaxy Training Network and covering topics related to nan
135+
button_link:
136+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html
137+
button_tip: View tutorial
138+
button_icon: tutorial
139+
- title_md: "Annotate, prepare tests and publish Galaxy workflows in workflow registries\n\
140+
\ (Visitors: 465)"
141+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
142+
on the Galaxy Training Network and covering topics related to nan
143+
button_link:
144+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html
145+
button_tip: View tutorial
146+
button_icon: tutorial
147+
- title_md: "Creating high resolution images of Galaxy Workflows\n (Visitors: 384)"
148+
description_md: Tutorial stored in Using Galaxy and Managing your Data topic
149+
on the Galaxy Training Network and covering topics related to nan
150+
button_link:
151+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-posters/tutorial.html
152+
button_tip: View tutorial
153+
button_icon: tutorial

‎communities/workflow4metabolomics/lab/sections/5_support_and_help.yml‎

Lines changed: 55 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,55 @@
1+
id: support
2+
title: Support & Help
3+
tabs:
4+
- id: help
5+
title: Help
6+
heading_md: >
7+
You can request help through different channels. If you think your problem might help other users as well,
8+
please post it in the Galaxy Help Forum. Please report tool bugs through our
9+
[support channel]({{ support_url }})
10+
and for specific questions feel free to reach out via the matrix chat.
11+
content:
12+
- title_md: Troubleshooting
13+
description_md: >
14+
Find specific advice for
15+
{gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)
16+
on the GTN.
17+
- title_md: Galaxy Support
18+
description_md: >
19+
Any user of Galaxy {{ site_name }} can request support online!
20+
button_md: Request support
21+
button_link: "{{ support_url }}"
22+
button_icon: help
23+
button_tip: Request support
24+
# - title_md: microGalaxy chat room
25+
# description_md: >
26+
# Chat with members of the microGalaxy community on Matrix
27+
# button_link: "{{ microgalaxy_matrix }}"
28+
# button_md: Matrix channel
29+
# button_icon: social
30+
# button_tip: Join the chat
31+
32+
- id: faq
33+
title: FAQ
34+
content:
35+
- title_md: How can I increase my storage quota?
36+
description_md: >
37+
Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
38+
button_md: Request
39+
button_link: "{{ quota_request_url }}"
40+
button_tip: Request quota
41+
button_icon: help
42+
- title_md: Can I upload sensitive data?
43+
description_md: >
44+
No, please do not upload personal or sensitive, such as human health or clinical data. Please see our
45+
[Privacy Policy]({{ data_policy_url }})
46+
page for definitions of sensitive and health-related information.
47+
48+
Please also make sure you have read our
49+
[Terms of Service]({{ terms_url }}),
50+
which covers hosting and analysis of research data.
51+
- title_md: Is my data private?
52+
description_md: >
53+
Please read our
54+
[Privacy Policy]({{ data_policy_url }})
55+
for information on your personal data and any data that you upload.

‎communities/workflow4metabolomics/lab/sections/6_community.yml‎

Lines changed: 67 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,67 @@
1+
id: community
2+
title: Community
3+
tabs:
4+
- id: participate
5+
title: Participate
6+
content:
7+
- title_md: Join our community!
8+
description_md: >
9+
This Galaxy space is the result of hard, collaborative work by many contributors.
10+
# It is maintained by the microGalaxy Community of Practice.
11+
# This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier.
12+
# Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)!
13+
# - title_md: Chat with others!
14+
# description_md: >
15+
# Use our matrix channel to chat with others from microGalaxy community
16+
# button_link: "{{ microgalaxy_matrix }}"
17+
# button_md:
18+
# button_tip: Visit microGalaxy
19+
# button_icon: social
20+
21+
- id: governance
22+
title: How is the Galaxy Community organised?
23+
heading_md: >
24+
Learn about the
25+
{gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN.
26+
content: []
27+
28+
- id: links
29+
title: Galaxy Community support links
30+
content:
31+
- title_md: "For general Galaxy support"
32+
description_md: "General Galaxy support"
33+
button_link: "{{ general_support }}"
34+
button_tip: Galaxy Support
35+
button_icon: help
36+
- title_md: "General Help Forum"
37+
description_md: "Access general Galaxy help"
38+
button_link: "{{ galaxy_help_url }}"
39+
button_tip: Help forum
40+
button_icon: help
41+
- title_md: "Galaxy Training Network Slack Workspace"
42+
description_md: "Join the GTN Slack community"
43+
button_link: "{{ gtn_slack_url }}"
44+
button_tip: Slack channel - Join the GTN Slack community.
45+
button_icon: social
46+
- title_md: "Galaxy Training Network Community Chat Room"
47+
description_md: "Connect on the GTN Matrix chat"
48+
button_link: "{{ gtn_matrix_channel }}"
49+
button_tip: Matrix channel - Connect on the GTN Matrix chat.
50+
button_icon: social
51+
# - title_md: "microGalaxy User Community Chat Room"
52+
# description_md: "Join the microGalaxy Matrix chat"
53+
# button_link: "{{ microgalaxy_matrix }}"
54+
# button_tip: Matrix channel - Join the microGalaxy Matrix chat.
55+
# button_icon: social
56+
- title_md: "General Galaxy Project Chat Room"
57+
description_md: "Join the Galaxy project chat"
58+
button_link: "{{ galaxy_matrix_channel }}"
59+
button_tip: Matrix channel - Join the Galaxy project chat.
60+
button_icon: social
61+
- title_md: "European Galaxy Server Chat Room"
62+
description_md: "Join the usegalaxy.eu chat"
63+
button_link: "{{ european_server_matrix_channel }}"
64+
button_tip: Matrix channel - Join the usegalaxy.eu chat.
65+
button_icon: social
66+
exclude_from:
67+
- usegalaxy.org.au

0 commit comments

Comments
 (0)