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Add new ro-crate exploration tuto #5260
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layout: faq-page | ||
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layout: tutorial_slides | ||
logo: "GTN" | ||
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title: "An earth-system RO-Crate" | ||
video: true | ||
questions: | ||
- "How to generate a RO-Crate" | ||
- "How to follow a Marine Omics study" | ||
- "How to read a RO-Crate ?" | ||
objectives: | ||
- "Understand RO-Crate in an earth-system context" | ||
time_estimation: 1H | ||
tags: | ||
- earth-system | ||
- ro-crate | ||
- ocean | ||
- marine omics | ||
key_points: | ||
- "RO-Crate in earth-system analysis" | ||
- "Marine omics workflow " | ||
contributors: | ||
- Marie59 | ||
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# Workflow context | ||
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The workflow used as an example here goes from : | ||
- First, produce a protein FASTA file from a nucleotide FASTA file using Prodigal (a tool that predicts protein-coding genes from DNA sequences). | ||
- Then, use InterProscan to create a tabular. Interproscan is a batch tool to query the InterPro database. It helps identify and predict the functions of proteins by comparing them to known databases. | ||
- Finally, discover SanntiS both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs). | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. maybe you can also link the tools? |
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## The workflow itself | ||
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![Marine Omics identifying biosynthetic gene clusters worflow image](./images/workflow_marino.png) | ||
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## Run the workflow | ||
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Import and run the following workflow https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. You can now embedd workflows. Have yout tried if this is working in slides? https://galaxyproject.org/news/2024-04-26-workflows-workflows-workflows/ |
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To know more on how to do that follow the tutorial https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Please try to use the Similar to |
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## Generate the RO-Crate | ||
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Once you run the workflow you can generate the RO-Crate. To do so follow the tutorial https://training.galaxyproject.org/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html | ||
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### From workflow to RO-Crate | ||
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![From workflow to RO-Crate](./images/workflow_rocrate.png) | ||
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### The RO-Crate folder and architecture | ||
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![From workflow to RO-Crate](./images/all_tree_structure.png) | ||
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### Let's dive into the ro-crate-metadata.json | ||
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![Date of RO-Crate creation and other informations](./images/rocrate1.png) | ||
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### Description of the RO-Crate structure | ||
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![Description of the RO-Crate structure](./images/rocrate2.png) | ||
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### Galaxy Provenance | ||
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![Date of RO-Crate creation and other informations](./images/rocrate3.png) | ||
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### Title and workflow details | ||
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![Title and details of the workflow](./images/rocrate4.png) | ||
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### Dates | ||
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![Dates of running the workflow and creation of the RO-Crate](./images/rocrate5.png) | ||
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### Data | ||
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![Data uploaded for the workflow and produced by it](./images/rocrate6.png) | ||
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### First tool Prodigal | ||
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![Details on Prodigal](./images/rocrate7.png) | ||
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### Second tool Regex Find and Replace | ||
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![Details on Regex Find and Replace](./images/rocrate8.png) | ||
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### Third tool InterProScan | ||
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![Details on InterProScan](./images/rocrate9.png) | ||
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### Fourth tool SanntiS to build Genbank | ||
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![Details on SanntiS to build Genbank](./images/rocrate10.png) | ||
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### Fourth tool SanntiS to annotate biosynthetic gene clusters | ||
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![Details on SanntiS to annotate biosynthetic gene clusters](./images/rocrate11.png) | ||
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### Details on the different files in the RO-Crate | ||
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![Details on the different files in the RO-Crate](./images/rocrate12.png) | ||
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### End of the ro-crate-metadata.json | ||
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![Details on the different files in the RO-Crate and end of the ro-crate-metadata.json](./images/rocrate13.png) | ||
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### Thank you! | ||
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Try to do the same on your workflow! | ||
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Maybe add EOSC as funders?