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shiltemann authored Sep 30, 2024
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2 changes: 1 addition & 1 deletion Gemfile.lock
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typhoeus (1.4.0)
ethon (>= 0.9.0)
unicode-display_width (2.5.0)
webrick (1.8.1)
webrick (1.8.2)
yell (2.2.2)
zeitwerk (2.6.12)

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topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md
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Gemfile.lock
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topics/assembly/tutorials/vgp_genome_assembly/tutorial.md
topics/community/tutorials/sig_define/tutorial.md
topics/dev/tutorials/community-tool-table/tutorial.md
topics/dev/tutorials/tool-annotation/tutorial.md
topics/dev/tutorials/tool-from-scratch/tutorial.md
topics/dev/tutorials/tool-generators-advanced/tutorial.md
topics/fair/tutorials/fair-data-registration/tutorial.md
topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.md
topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.md
topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md
topics/single-cell/tutorials/GO-enrichment/tutorial.md
topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.md
topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.md
topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.md
topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.md
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topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.md
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_layouts/event.html
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.github/workflows/ci-main.yml
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_config.yml
assets/js/main.js
assets/js/tutorial-mode.js
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topics/data-science/tutorials/sql-advanced/tutorial.md
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_plugins/jekyll-jsonld.rb
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_config.yml
assets/js/main.js
assets/js/tutorial-mode.js
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_config.yml
faqs/galaxy/workflows_best_practices.md
topics/fair/tutorials/ro-crate-galaxy-best-practices/img/workflow-entry.png
topics/fair/tutorials/ro-crate-galaxy-best-practices/img/workflow-invocation.png
topics/fair/tutorials/ro-crate-galaxy-best-practices/img/workflow-run-page.png
topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.md
topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.md
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topics/assembly/tutorials/assembly-decontamination/tutorial.md
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topics/microbiome/tutorials/dada-16S/tutorial.md
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topics/assembly/tutorials/mitochondrion-assembly/tutorial.md
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_plugins/jekyll-jsonld.rb
_plugins/util.rb
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_layouts/event-track.html
events/galaxy-academy-2024.md
events/tracks/gta2024-assembly.md
events/tracks/gta2024-bacterial-genomics.md
events/tracks/gta2024-bycovid.md
events/tracks/gta2024-microbiome.md
events/tracks/gta2024-ml.md
events/tracks/gta2024-proteomics.md
events/tracks/gta2024-single-cell.md
events/tracks/gta2024-transcriptomics.md
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bin/lint.rb
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bin/news.rb
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topics/admin/tutorials/interactive-tools/slides.html
topics/admin/tutorials/interactive-tools/tutorial.md
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topics/microbiome/tutorials/diversity/tutorial.md
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topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md
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metadata/workflowhub.yml
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_includes/instance-dropdown.html
_layouts/topic.html
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topics/ecology/tutorials/Ecoregionalization_tutorial/Images/2_example.png
topics/ecology/tutorials/Ecoregionalization_tutorial/Images/BRT-Echinodermata_Crinoidea_Comatulida_Antedonidae_Florometra_mawsoni__pred_plot.png
topics/ecology/tutorials/Ecoregionalization_tutorial/Images/JLN_param_example.png
topics/ecology/tutorials/Ecoregionalization_tutorial/Images/Map.png
topics/ecology/tutorials/Ecoregionalization_tutorial/Images/NA_example.png
topics/ecology/tutorials/Ecoregionalization_tutorial/Images/advanced_out_example.png
topics/ecology/tutorials/Ecoregionalization_tutorial/Images/pivot_file_example.png
topics/single-cell/images/GO-enrichment/slides_images/components_5.png
topics/single-cell/images/GO-enrichment/slides_images/enrichment_7.png
topics/single-cell/images/GO-enrichment/slides_images/example1_16.png
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topics/single-cell/images/GO-enrichment/slides_images/ontology_2.png
topics/single-cell/images/GO-enrichment/slides_images/purpose_19.png
topics/single-cell/images/GO-enrichment/slides_images/roadmap_1.png
topics/single-cell/images/GO-enrichment/slides_images/step1_9.png
topics/single-cell/images/GO-enrichment/slides_images/step2_10.png
topics/single-cell/images/GO-enrichment/slides_images/step3_11.png
topics/single-cell/images/GO-enrichment/slides_images/step4_12.png
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topics/single-cell/images/GO-enrichment/slides_images/step6_14.png
topics/single-cell/images/GO-enrichment/slides_images/step7_15.png
topics/single-cell/images/scrna-scanpy-pbmc3k/dotplot_annotated_clusters.png
topics/single-cell/images/scrna-scanpy-pbmc3k/qc_violin_plot.png
topics/single-cell/images/scrna-scanpy-pbmc3k/umap_after_clustering.png
topics/single-cell/images/scrna-scanpy-pbmc3k/umap_annotated_clusters.png
topics/single-cell/images/scrna-scanpy-pbmc3k/umap_before_clustering.png
topics/single-cell/images/scrna-scanpy-pbmc3k/umap_plot_marker_genes.png
topics/single-cell/images/scrna-scanpy-pbmc3k/violin_plot_marker_genes.png
topics/single-cell/images/scrna-scanpy-pbmc3k/violin_plot_rank_genes_groups_CST3_NKG7_PPBP.png
topics/single-cell/images/workflow.png
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metadata/git-mod-efc7be5ba874506b92c304fa69236167ebd2e82a.txt
metadata/git-pub-efc7be5ba874506b92c304fa69236167ebd2e82a.txt
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metadata/shortlinks.yaml
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topics/introduction/tutorials/galaxy-intro-101/tutorial.md
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A assets/js/tutorial-mode.js
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R099 metadata/git-pub-b5acaf862a6ef65d9660d4ea2d6152029e21f078.txt metadata/git-pub-efc7be5ba874506b92c304fa69236167ebd2e82a.txt
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A topics/single-cell/faqs/gtn-in-galaxy_mode-cs.md
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137 changes: 69 additions & 68 deletions topics/assembly/tutorials/vgp_genome_assembly/tutorial.md
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Expand Up @@ -548,34 +548,34 @@ Let's use gfastats to get a basic idea of what our assembly looks like. We'll ru
>
> 2. Rename outputs of `gfastats` step to as `Hap1 stats` and `Hap2 stats`
>
> > > This would generate summary files that look like this (only the first six rows are shown):
> > >
> > > ```
> > > Expected genome size 11747160
> > > # scaffolds 0
> > > Total scaffold length 0
> > > Average scaffold length nan
> > > Scaffold N50 0
> > > Scaffold auN 0.00
> > > ```
> > >
> > > Because we ran `gfastats` on hap1 and hap2 outputs of `hifiasm` we need to join the two outputs together for easier interpretation:
> This would generate summary files that look like this (only the first six rows are shown):
>
> ```
> Expected genome size 11747160
> # scaffolds 0
> Total scaffold length 0
> Average scaffold length nan
> Scaffold N50 0
> Scaffold auN 0.00
> ```
>
> Because we ran `gfastats` on hap1 and hap2 outputs of `hifiasm` we need to join the two outputs together for easier interpretation:
>
> 3. Run {% tool [Column join](toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3) %} with the following parameters:
> - {% icon param-files %} *"Input file"*: select `Hap1 stats` and the `Hap2 stats` datasets. Keep all other settings as they are.
>
> 4. Rename the output as `gfastats on hap1 and hap2 (full)`
>
> > > This would generate a joined summary file that looks like this (only the first five rows are shown):
> > >
> > > ```
> > > # gaps 0 0
> > > # gaps in scaffolds 0 0
> > > # paths 0 0
> > > # segments 17 16
> > > ```
> > >
> > > Now let's extract only relevant information by excluding all lines containing the word `scaffold` since there are no scaffolds at this stage of the assembly process (only contigs):
> This would generate a joined summary file that looks like this (only the first five rows are shown):
>
> ```
> # gaps 0 0
> # gaps in scaffolds 0 0
> # paths 0 0
> # segments 17 16
> ```
>
> Now let's extract only relevant information by excluding all lines containing the word `scaffold` since there are no scaffolds at this stage of the assembly process (only contigs):
>
> 5. Run {% tool [Search in textfiles](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1) %} with the following parameters:
> - {% icon param-files %} *"Input file"*: select `gfastats on hap1 and hap2 (full)`
Expand Down Expand Up @@ -756,35 +756,35 @@ Let's use gfastats to get a basic idea of what our assembly looks like. We'll ru
>
> 2. Rename outputs of `gfastats` step to as `Primary stats` and `Alternate stats`
>
> > > This would generate summary files that look like this (only the first six rows are shown):
> > >
> > > ```
> > > Expected genome size 11747160
> > > # scaffolds 25
> > > Total scaffold length 18519764
> > > Average scaffold length 740790.56
> > > Scaffold N50 813311
> > > Scaffold auN 913050.77
> > > ```
> > >
> > > Because we ran `gfastats` on Primary and Alternate outputs of `hifiasm` we need to join the two outputs together for easier interpretation:
> This would generate summary files that look like this (only the first six rows are shown):
>
> ```
> Expected genome size 11747160
> # scaffolds 25
> Total scaffold length 18519764
> Average scaffold length 740790.56
> Scaffold N50 813311
> Scaffold auN 913050.77
> ```
>
> Because we ran `gfastats` on Primary and Alternate outputs of `hifiasm` we need to join the two outputs together for easier interpretation:
>
> 3. Run {% tool [Column join](toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3) %} with the following parameters:
> - {% icon param-files %} *"Input file"*: select `Primary stats` and the `Alternate stats` datasets (these are from **Step 2** above). Keep all other setting as they are.
>
> 4. Rename the output as `gfastats on Pri and Alt (full)`
>
> > > This would generate a joined summary file that looks like this (only five rows are shown):
> > >
> > > ```
> > > # contigs 25 10
> > > # dead ends . 16
> > > # disconnected components . 7
> > > # edges . 6
> > > # gaps 0 0
> > > ```
> > >
> > > Now let's extract only relevant information by excluding all lines containing the word `scaffold` since there are no scaffolds at this stage of the assembly process (only contigs):
> This would generate a joined summary file that looks like this (only five rows are shown):
>
> ```
> # contigs 25 10
> # dead ends . 16
> # disconnected components . 7
> # edges . 6
> # gaps 0 0
> ```
>
> Now let's extract only relevant information by excluding all lines containing the word `scaffold` since there are no scaffolds at this stage of the assembly process (only contigs):
>
> 5. Run {% tool [Search in textfiles](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1) %} with the following parameters:
> - {% icon param-files %} *"Input file"*: select `gfastats on Pri and Alt (full)`
Expand Down Expand Up @@ -876,7 +876,7 @@ Despite BUSCO being robust for species that have been widely studied, it can be
> - {% icon param-file %} *"First genome assembly"*: `Primary contigs FASTA`
> - {% icon param-file %} *"Second genome assembly"*: `Alternate contigs FASTA`
>
> > > (REMINDER: `Primary contigs FASTA` and `Alternate contigs FASTA` were generated [earlier](#gfa2fasta_solo))
> (REMINDER: `Primary contigs FASTA` and `Alternate contigs FASTA` were generated [earlier](#gfa2fasta_solo))
>
{: .hands_on}
Expand Down Expand Up @@ -913,23 +913,24 @@ The first relevant parameter is the `Estimated genome size`.
> <hands-on-title>Get estimated genome size</hands-on-title>
>
> 1. Look at the `GenomeScope summary` output (generated during *k*-mer profiling [step](#genome-profiling-with-genomescope2)). The file should have content that looks like this (it may not be exactly like this):
> > ```
> > GenomeScope version 2.0
> > input file = ....
> > output directory = .
> > p = 2
> > k = 31
> > TESTING set to TRUE
> >
> > property min max
> > Homozygous (aa) 99.4165% 99.4241%
> > Heterozygous (ab) 0.575891% 0.583546%
> > Genome Haploid Length 11,739,321 bp 11,747,160 bp
> > Genome Repeat Length 722,921 bp 723,404 bp
> > Genome Unique Length 11,016,399 bp 11,023,755 bp
> > Model Fit 92.5159% 96.5191%
> > Read Error Rate 0.000943206% 0.000943206%
> > ```
>
> ```
> GenomeScope version 2.0
> input file = ....
> output directory = .
> p = 2
> k = 31
> TESTING set to TRUE
>
> property min max
> Homozygous (aa) 99.4165% 99.4241%
> Heterozygous (ab) 0.575891% 0.583546%
> Genome Haploid Length 11,739,321 bp 11,747,160 bp
> Genome Repeat Length 722,921 bp 723,404 bp
> Genome Unique Length 11,016,399 bp 11,023,755 bp
> Model Fit 92.5159% 96.5191%
> Read Error Rate 0.000943206% 0.000943206%
> ```
>
> 2. Copy the number value for the maximum Genome Haploid Length to your clipboard (CTRL + C on Windows; CMD + C on MacOS).
> 3. Click on "Upload Data" in the toolbox on the left.
Expand Down Expand Up @@ -992,7 +993,7 @@ Now let's parse the `transition between haploid & diploid` and `upper bound for
> >
> {: .question}
>
> > Now let's get the transition parameter.
> Now let's get the transition parameter.
>
> 5. Run {% tool [Advanced Cut](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0) %} with the following parameters:
> - {% icon param-file %} *"File to cut"*: `Parsing purge parameters`
Expand Down Expand Up @@ -1318,11 +1319,11 @@ Before we begin, we need to upload BioNano data:
>
> 1. Copy the following URLs into clipboard. You can do this by clicking on {% icon copy %} button in the right upper corner of the box below. It will appear if you mouse over the box.
>
> > ```
> > https://zenodo.org/records/5887339/files/bionano.cmap
> > ```
> ```
> https://zenodo.org/records/5887339/files/bionano.cmap
> ```
>
> 2. Upload datasets into Galaxy
> 2. Upload datasets into Galaxy
> - set the datatype to `cmap`
>
> {% snippet faqs/galaxy/datasets_import_via_link.md format="cmap" %}
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Expand Up @@ -37,6 +37,8 @@ follow_up_training:
- sig_create
---

In Galaxy, the term *[Special Interest Group](https://galaxyproject.org/community/sig)* (**SIG**) refers to a dedicated scientific community that crosses individual lab boundaries and wants to collaborate, share resources, support each other, and/or collectively advocate on a given theme. We have **SIGs** based on [**region**](https://galaxyproject.org/community/sig/#regional-communities), [**domain of science**](https://galaxyproject.org/community/sig/#communities-of-practice), and more. You might consider that a **SIG** covers any group of like-minded Galaxy enthusiasts not currently combined into a [**Working Group**](https://galaxyproject.org/community/wg/).

> <agenda-title></agenda-title>
>
> In this tutorial, we will cover:
Expand All @@ -46,10 +48,6 @@ follow_up_training:
>
{: .agenda}

# Special Interest Groups

In Galaxy, the term *[Special Interest Group](https://galaxyproject.org/community/sig)* (**SIG**) refers to a dedicated scientific community that crosses individual lab boundaries and wants to collaborate, share resources, support each other, and/or collectively advocate on a given theme. We have **SIGs** based on [**region**](https://galaxyproject.org/community/sig/#regional-communities), [**domain of science**](https://galaxyproject.org/community/sig/#communities-of-practice), and more. You might consider that a **SIG** covers any group of like-minded Galaxy enthusiasts not currently combined into a [**Working Group**](https://galaxyproject.org/community/wg/).

<div class='right'><img src="../../images/mind_map.svg" alt="Person looking at a diagram with a central rectangle connected to many other nodes representing people and connections" width="25" /></div>

You can find a directory of current [**SIGs** below](https://galaxyproject.org/community/sig/).
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