diff --git a/topics/fair/tutorials/earth_system_rocrate/slides.html b/topics/fair/tutorials/earth_system_rocrate/slides.html index ef1ce9f5089fa9..bfc463cf0447d2 100644 --- a/topics/fair/tutorials/earth_system_rocrate/slides.html +++ b/topics/fair/tutorials/earth_system_rocrate/slides.html @@ -19,17 +19,20 @@ key_points: - "RO-Crate in earth-system analysis" - "Marine omics workflow " -contributors: - - Marie59 - +contributions: + authorship: + - Marie59 + funding: + - fairease + - eurosciencegateway --- # Workflow context 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). +- First, produce a protein FASTA file from a nucleotide FASTA file using [Prodigal](tool_id=toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0) (a tool that predicts protein-coding genes from DNA sequences). +- Then, use [InterProscan](toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3) 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](toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1) both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs). --- ## The workflow itself @@ -39,15 +42,15 @@ ## Run the workflow -Import and run the following workflow https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters +Import and run the [Biosynthetic Gene Clusters workflow]({% https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters %}) -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 +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 %}) --- ## Generate the RO-Crate -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 +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 %}) ---