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Lab updates #196

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Lab updates #196

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655c542
Strip AU content from genome lab templates
neoformit Oct 18, 2024
76fc7d8
Strip AU content from genome lab
neoformit Oct 18, 2024
64ecda5
Strip AU content from Proteomics lab
neoformit Oct 18, 2024
5ab0f8c
Strip AU content from SPOC lab
neoformit Oct 18, 2024
7e2d8ca
Merge branch 'main' of https://github.com/galaxyproject/galaxy_codex …
neoformit Nov 18, 2024
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47 changes: 31 additions & 16 deletions communities/genome/lab/annotation.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ tabs:
- title_md: <code>RepeatMasker</code> - screen DNA sequences for interspersed repeats and low complexity regions
description_md: >
<p>
RepeatMasker is a program that screens DNA for repeated elements such as tandem repeats, transposons, SINEs and LINEs. Galaxy AU has installed the full and curated DFam screening databases, or a custom database can be provided in <code>fasta</code> format. Additional reference data can be downloaded from <a href="https://www.girinst.org/repbase/" target="_blank"> RepBase</a>.
RepeatMasker is a program that screens DNA for repeated elements such as tandem repeats, transposons, SINEs and LINEs. Galaxy {{ site_name }} should have the full and curated DFam screening databases, or a custom database can be provided in <code>fasta</code> format. Additional reference data can be downloaded from <a href="https://www.girinst.org/repbase/" target="_blank"> RepBase</a>.
</p>
inputs:
- datatypes:
Expand Down Expand Up @@ -109,6 +109,9 @@ tabs:
- fasta
label: Repeat-masked (hard) genome assembly
button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=fgenesh_annotate&version=latest"
exclude_from:
- usegalaxy.org
- usegalaxy.eu

- id: workflows
title: Workflows
Expand Down Expand Up @@ -138,7 +141,7 @@ tabs:
button_link: "{{ galaxy_base_url }}/u/anna/w/genome-annotation-with-maker"
view_link: ''
view_tip: ''
button_tip: Run in Galaxy AU
button_tip: Run in Galaxy {{ site_name}}
- title_md: Annotation with Funannotate
description_md: >
<p>
Expand All @@ -160,15 +163,18 @@ tabs:
button_link: "{{ galaxy_base_url }}/u/anna/w/annotation-funannotate"
view_link: ''
view_tip: ''
button_tip: Run in Galaxy AU
button_tip: Run in Galaxy {{ site_name }}

- id: tsi_transcripts
title: Transcript alignment
content:
- title_md: About these workflows
description_md: >
<p>
This <a href="https://australianbiocommons.github.io/how-to-guides/genome_annotation/Transcriptome" target="_blank"> How-to-Guide </a> will describe the steps required to align transcript data to your genome on the Galaxy Australia platform, using multiple workflows. The outputs from these workflows can then be used as inputs into the next annotation workflow using FgenesH++.
This <a href="https://australianbiocommons.github.io/how-to-guides/genome_annotation/Transcriptome" target="_blank"> How-to-Guide </a> will describe the steps required to align transcript data to your genome on Galaxy, using multiple workflows.
{% if site_name == 'Australia' %}
The outputs from these workflows can then be used as inputs into the next annotation workflow using FgenesH++.
{% endif %}
</p>
- title_md: Repeat masking
description_md: >
Expand All @@ -182,7 +188,7 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=875"
view_link: https://workflowhub.eu/workflows/875
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}

- title_md: QC and trimming of RNAseq
description_md: >
Expand All @@ -196,7 +202,7 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=876"
view_link: https://workflowhub.eu/workflows/876
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}

- title_md: Find transcripts
description_md: >
Expand All @@ -212,7 +218,7 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=877"
view_link: https://workflowhub.eu/workflows/877
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}

- title_md: Combine transcripts
description_md: >
Expand All @@ -230,7 +236,7 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=878"
view_link: https://workflowhub.eu/workflows/878
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}

- title_md: Extract transcripts
description_md: >
Expand All @@ -244,7 +250,7 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=879"
view_link: https://workflowhub.eu/workflows/879
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}


- title_md: Convert formats
Expand All @@ -260,15 +266,15 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=880"
view_link: https://workflowhub.eu/workflows/880
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}

- id: tsi_annotation
title: Annotation with FgenesH++
content:
- title_md: About these workflows
description_md: >
<p>
This <a href="https://australianbiocommons.github.io/how-to-guides/genome_annotation/Fgenesh" target="_blank"> How-to-Guide </a> will describe the steps required to annotate your genome on the Galaxy Australia platform, using multiple workflows.
This <a href="https://australianbiocommons.github.io/how-to-guides/genome_annotation/Fgenesh" target="_blank"> How-to-Guide </a> will describe the steps required to annotate your genome on Galaxy, using multiple workflows.
</p>
- title_md: Annotation with FgenesH++
description_md: >
Expand Down Expand Up @@ -297,7 +303,10 @@ tabs:
button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=881"
view_link: https://workflowhub.eu/workflows/881
view_tip: View in WorkflowHub
button_tip: Import to Galaxy Australia
button_tip: Import to Galaxy {{ site_name }}
exclude_from:
- usegalaxy.org
- usegalaxy.eu

- id: help
title: Help
Expand All @@ -312,7 +321,7 @@ tabs:
<p>
The flowchart below shows how you might use your input data (in green) with different Galaxy tools (in blue) to annotate a genome assembly. For example, one pathway would be taking an assembled genome, plus information about repeats, and data from RNA-seq, to run in the Maker pipeline. The annotatations can then be viewed in JBrowse.
</p>
<img class="img-fluid" src="./static/annotation-overview.png" alt="Genome annotation flowchart">
<img class="img-fluid" src="https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/genome/lab/static/annotation-overview.png" alt="Genome annotation flowchart">
<p class="text-center">
A graphical representation of genome annotation
</p>
Expand All @@ -324,6 +333,9 @@ tabs:
button_md: Apply
button_link: https://site.usegalaxy.org.au/request/access/fgenesh
button_tip: Apply for access to Fgenesh++
exclude_from:
- usegalaxy.org
- usegalaxy.eu
- title_md: Can I use Apollo to share and edit the annotated genome?
description_md: >
<p>
Expand All @@ -337,6 +349,9 @@ tabs:
</p>
button_md: More info
button_link: https://support.biocommons.org.au/support/solutions/articles/6000244843-apollo-for-collaborative-curation-and-editing
exclude_from:
- usegalaxy.org
- usegalaxy.eu
- title_md: Tutorials
description_md: >
<p class="lead">
Expand All @@ -352,10 +367,10 @@ tabs:
<p>
This <a href="https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/tutorial.html" target="_blank"> Galaxy tutorial </a> provides a complete walkthrough of the process of annotation with Funannotate, including the preparation of RNAseq data, structural annotation, functional annotation, visualisation, and comparing annotations.
</p>
- title_md: Galaxy Australia support
- title_md: Galaxy support
description_md: >
<p>
Any user of Galaxy Australia can request support through an online form.
Any user of Galaxy {{ site_name }} can request support through an online form.
</p>
button_md: Request support
button_link: /request/support
button_link: "{{ support_url }}"
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