microgalaxy community resources update

Author: scorreard

communities/microgalaxy/lab/sections/2_microbial_isolates.yml

@@ -503,6 +503,16 @@ tabs:
   title: Tutorials
   heading_md: Tutorials to train you to perform microbial data analysis
   content:
+  - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and 
+      optionally Illumina data)
+    description_md: Tutorial stored in Assembly topic on the Galaxy Training 
+      Network and covering topics related to Sequence assembly, Whole genome 
+      sequencing, Public health and epidemiology, Genomics, Microbiology, 
+      Antimicrobial resistance
+    button_link: 
+      https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html
+    button_tip: View tutorial
+    button_icon: tutorial
   - title_md: Making sense of a newly assembled genome
     description_md: Tutorial stored in Assembly topic on the Galaxy Training 
       Network and covering topics related to Sequence assembly, Genomics, 
@@ -519,30 +529,20 @@ tabs:
       https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Genome Assembly of a bacterial genome (MRSA) sequenced using 
-      Illumina MiSeq Data
-    description_md: Tutorial stored in Assembly topic on the Galaxy Training 
-      Network and covering topics related to Sequence assembly, Whole genome 
-      sequencing, Public health and epidemiology, Genomics, Microbiology
-    button_link: 
-      https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html
-    button_tip: View tutorial
-    button_icon: tutorial
   - title_md: Assembly of metagenomic sequencing data
     description_md: Tutorial stored in Assembly topic on the Galaxy Training 
       Network and covering topics related to Metagenomics, Sequence assembly
     button_link: 
       https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and 
-      optionally Illumina data)
+  - title_md: Genome Assembly of a bacterial genome (MRSA) sequenced using 
+      Illumina MiSeq Data
     description_md: Tutorial stored in Assembly topic on the Galaxy Training 
       Network and covering topics related to Sequence assembly, Whole genome 
-      sequencing, Public health and epidemiology, Genomics, Microbiology, 
-      Antimicrobial resistance
+      sequencing, Public health and epidemiology, Genomics, Microbiology
     button_link: 
-      https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html
+      https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: Checking expected species and contamination in bacterial isolate
@@ -585,21 +585,21 @@ tabs:
       https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Refining Genome Annotations with Apollo (prokaryotes)
+  - title_md: Bacterial Genome Annotation
     description_md: Tutorial stored in Genome Annotation topic on the Galaxy 
       Training Network and covering topics related to Genomics, Microbiology, 
-      Gene and protein families, Sequence analysis
+      Gene and protein families, Sequence analysis, Whole genome sequencing, 
+      Functional genomics, Mobile genetic elements
     button_link: 
-      https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html
+      https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Bacterial Genome Annotation
+  - title_md: Refining Genome Annotations with Apollo (prokaryotes)
     description_md: Tutorial stored in Genome Annotation topic on the Galaxy 
       Training Network and covering topics related to Genomics, Microbiology, 
-      Gene and protein families, Sequence analysis, Whole genome sequencing, 
-      Functional genomics, Mobile genetic elements
+      Gene and protein families, Sequence analysis
     button_link: 
-      https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html
+      https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: Identification of AMR genes in an assembled bacterial genome
@@ -611,18 +611,18 @@ tabs:
       https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Bacterial genome quality control
+  - title_md: Dataset construction for bacterial comparative genomics
     description_md: Tutorial stored in Genome Annotation topic on the Galaxy 
       Training Network and covering topics related to Genomics, Microbiology
     button_link: 
-      https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html
+      https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Dataset construction for bacterial comparative genomics
+  - title_md: Bacterial genome quality control
     description_md: Tutorial stored in Genome Annotation topic on the Galaxy 
       Training Network and covering topics related to Genomics, Microbiology
     button_link: 
-      https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html
+      https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: Comparative gene analysis in unannotated genomes
@@ -659,36 +659,36 @@ tabs:
       https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: 'metaQuantome 1: Data creation'
+  - title_md: 'metaQuantome 3: Taxonomy'
     description_md: Tutorial stored in Proteomics topic on the Galaxy Training 
       Network and covering topics related to Proteomics, Proteogenomics, 
-      Biodiversity, Taxonomy
+      Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy
     button_link: 
-      https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html
+      https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Metaproteomics tutorial
+  - title_md: 'metaQuantome 1: Data creation'
     description_md: Tutorial stored in Proteomics topic on the Galaxy Training 
       Network and covering topics related to Proteomics, Proteogenomics, 
       Biodiversity, Taxonomy
     button_link: 
-      https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html
+      https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: 'metaQuantome 3: Taxonomy'
+  - title_md: 'metaQuantome 2: Function'
     description_md: Tutorial stored in Proteomics topic on the Galaxy Training 
       Network and covering topics related to Proteomics, Proteogenomics, 
-      Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy
+      Metatranscriptomics, Microbial ecology, Metagenomics
     button_link: 
-      https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html
+      https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: 'metaQuantome 2: Function'
+  - title_md: Metaproteomics tutorial
     description_md: Tutorial stored in Proteomics topic on the Galaxy Training 
       Network and covering topics related to Proteomics, Proteogenomics, 
-      Metatranscriptomics, Microbial ecology, Metagenomics
+      Biodiversity, Taxonomy
     button_link: 
-      https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html
+      https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: Quality and contamination control in bacterial isolate using 

communities/microgalaxy/lab/sections/3_microbiome.yml

@@ -562,12 +562,13 @@ tabs:
       https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short)
+  - title_md: Pathogen detection from (direct Nanopore) sequencing data using 
+      Galaxy - Foodborne Edition
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Metatranscriptomics, Microbial 
-      ecology, Taxonomy, Function analysis, Sequence analysis
+      Network and covering topics related to Metagenomics, Public health and 
+      epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: Taxonomic Profiling and Visualization of Metagenomic Data
@@ -578,6 +579,14 @@ tabs:
       https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
+  - title_md: Metatranscriptomics analysis using microbiome RNA-seq data
+    description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
+      Network and covering topics related to Metatranscriptomics, Microbial 
+      ecology, Taxonomy, Function analysis, Sequence analysis
+    button_link: 
+      https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html
+    button_tip: View tutorial
+    button_icon: tutorial
   - title_md: Antibiotic resistance detection
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
       Network and covering topics related to Metagenomic sequencing, Public 
@@ -595,68 +604,59 @@ tabs:
       https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Binning of metagenomic sequencing data
-    description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Metagenomics, Sequence assembly
-    button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html
-    button_tip: View tutorial
-    button_icon: tutorial
-  - title_md: Remove contamination and host reads
+  - title_md: Identification of the micro-organisms in a beer using Nanopore 
+      sequencing
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to nan
+      Network and covering topics related to Metagenomics, Microbial ecology, 
+      Taxonomy, Sequence analysis
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Metatranscriptomics analysis using microbiome RNA-seq data
+  - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short)
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
       Network and covering topics related to Metatranscriptomics, Microbial 
       ecology, Taxonomy, Function analysis, Sequence analysis
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Building an amplicon sequence variant (ASV) table from 16S data 
-      using DADA2
+  - title_md: Remove contamination and host reads
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Microbial ecology, Taxonomy, 
-      Sequence analysis, Metabarcoding
+      Network and covering topics related to nan
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Assembly of metagenomic sequencing data
+  - title_md: Binning of metagenomic sequencing data
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
       Network and covering topics related to Metagenomics, Sequence assembly
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Identification of the micro-organisms in a beer using Nanopore 
-      sequencing
+  - title_md: Assembly of metagenomic sequencing data
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Metagenomics, Microbial ecology, 
-      Taxonomy, Sequence analysis
+      Network and covering topics related to Metagenomics, Sequence assembly
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Pathogen detection from (direct Nanopore) sequencing data using 
-      Galaxy - Foodborne Edition
+  - title_md: Building an amplicon sequence variant (ASV) table from 16S data 
+      using DADA2
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Metagenomics, Public health and 
-      epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis
+      Network and covering topics related to Microbial ecology, Taxonomy, 
+      Sequence analysis, Metabarcoding
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: Building and Annotating Metagenome-Assembled Genomes (MAGs) from 
-      Short Metagenomics Paired Reads
+  - title_md: QIIME 2 Moving Pictures
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Metagenomics, Sequence assembly
+      Network and covering topics related to Microbial ecology, Taxonomy, 
+      Sequence analysis, Metabarcoding
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: QIIME 2 Cancer Microbiome Intervention
@@ -667,12 +667,12 @@ tabs:
       https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: QIIME 2 Moving Pictures
+  - title_md: Building and Annotating Metagenome-Assembled Genomes (MAGs) from 
+      Short Metagenomics Paired Reads
     description_md: Tutorial stored in Microbiome topic on the Galaxy Training 
-      Network and covering topics related to Microbial ecology, Taxonomy, 
-      Sequence analysis, Metabarcoding
+      Network and covering topics related to Metagenomics, Sequence assembly
     button_link: 
-      https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html
+      https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: 16S Microbial Analysis with mothur (extended)