From be94e6efb0b6a8dd727533a2c2e9ec66183be213 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Sun, 9 Jul 2023 02:17:21 +0200 Subject: [PATCH 1/3] =?UTF-8?q?pride=20month=20over=20=F0=9F=8C=88?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- _config.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/_config.yml b/_config.yml index 1ce899f47be815..9207052df383dc 100644 --- a/_config.yml +++ b/_config.yml @@ -244,16 +244,16 @@ plugins: - jekyll-redirect-from # An announcement to display on the home page -announcement: - class: success - title: GTN Celebrates Pride Month - text: | - June is pride month in many countries around the world! The GTN is celebrating it by remembering the story of Alan L. Hart, a trans doctor who pioneered the use of x-ray photography in tuberculosis detection. - - [Read about Alan L. Hart's contribution to M. Tuberculosis](/training-material/news/2023/06/01/hart.html){: .btn.btn-primary} - Activate the GTN Theme! - - Note: You can change your theme any time via the 'Extras' menu at the top! +#announcement: +# class: success +# title: GTN Celebrates Pride Month +# text: | +# June is pride month in many countries around the world! The GTN is celebrating it by remembering the story of Alan L. Hart, a trans doctor who pioneered the use of x-ray photography in tuberculosis detection. +# +# [Read about Alan L. Hart's contribution to M. Tuberculosis](/training-material/news/2023/06/01/hart.html){: .btn.btn-primary} +# Activate the GTN Theme! +# +# Note: You can change your theme any time via the 'Extras' menu at the top! # A banner image that can be displayed separately for short wide banner images. Alt text is mandatory. # banner_image: From d44643e11e471f33e099f3af36373bc96cbd49f6 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Sun, 9 Jul 2023 02:25:16 +0200 Subject: [PATCH 2/3] Fix a handful of broken snippets --- .github/workflows/ci.yml | 4 + .../tutorials/largegenome/tutorial.md | 2 + .../tutorials/atac-seq/tutorial.md | 3 + .../tutorials/gc_ms_with_xcms/tutorial.md | 80 +++++++++---------- .../rna-seq-bash-star-align/tutorial.md | 11 ++- 5 files changed, 54 insertions(+), 46 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b11c49a1958092..7b00a0e98c33f0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -71,6 +71,10 @@ jobs: --enforce-https=false \ ./_site + - name: Ensure no unexpected encoded HTML in output + run: | + fgrep -R 'lt;blockquote' _site + - name: Run aXe accessibility testing on some representative URLs run: | node_modules/.bin/http-server _site/ & diff --git a/topics/assembly/tutorials/largegenome/tutorial.md b/topics/assembly/tutorials/largegenome/tutorial.md index 0685d89fbc5d14..c1ee211715e72e 100644 --- a/topics/assembly/tutorials/largegenome/tutorial.md +++ b/topics/assembly/tutorials/largegenome/tutorial.md @@ -147,7 +147,9 @@ We are also using a reference genome *Arabidopsis thaliana* for a later comparis > {% snippet faqs/galaxy/datasets_import_from_data_library.md %} > > 3. Check that the datatypes for the three files of sequencing reads are `fastq.gz`, not `fastqsanger.gz` and change datatype if needed. +> > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %} +> {: .hands_on} * This tutorial uses these input files and gives some examples from the results. diff --git a/topics/epigenetics/tutorials/atac-seq/tutorial.md b/topics/epigenetics/tutorials/atac-seq/tutorial.md index 09974ed8fa2a34..8c3a63535cc377 100644 --- a/topics/epigenetics/tutorials/atac-seq/tutorial.md +++ b/topics/epigenetics/tutorials/atac-seq/tutorial.md @@ -438,8 +438,11 @@ Because of the PCR amplification, there might be read duplicates (different read > - {% icon param-file %} *"Select lines from"*: Select the output of **MarkDuplicates** {% icon tool %} > - *"that*: `Matching` > - *"the pattern*: `(Library|LIBRARY)` +> > 2. Check that the datatype is tabular. If not, change it. +> > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="tabular" %} +> > 3. {% tool [Transpose rows/columns in a tabular file](toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0) %}: > - {% icon param-file %} *"Select lines from"*: Select the output of **Select** {% icon tool %} > diff --git a/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.md b/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.md index 917ff51c0409e2..d74747ca40d919 100644 --- a/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.md +++ b/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.md @@ -326,46 +326,46 @@ The spectral data comes as an `.msp` file, which is a text file structured accor > Data Exploration > -> Click *"View data"* {% icon galaxy-eye %} icon next to the dataset in the Galaxy history. The contents of the file would look like this: -> -> {% snippet faqs/galaxy/datasets_icons.md %} -> -> ``` -> NAME:C001 -> IONMODE:Negative -> SPECTRUMTYPE:Centroid -> RETENTIONTIME:383.27 -> Num Peaks:231 -> 217.1073 64041926 -> 243.0865 35597866 -> 257.1134 31831229 -> 224.061 27258239 -> 258.11 24996353 -> 241.0821 23957171 -> 315.1188 13756744 -> ... -> -> NAME:C002 -> IONMODE:Negative -> SPECTRUMTYPE:Centroid -> RETENTIONTIME:281.62 -> Num Peaks:165 -> 307.1573 299174880 -> 147.0654 298860831 -> 149.0447 287809889 -> 218.1066 118274758 -> 189.076 112486871 -> 364.1787 75134143 -> 191.0916 52526567 -> 308.1579 52057158 -> ... -> ``` -> -> > Negative ion mode -> > -> > You might wonder how can the ionisation mode (_IONMODE_) for GC-MS data be negative when using electron impact (EI+) ionization. This is, of course, incorrect. This is actually just a default behaviour of **RAMClustR**. We can optionally change this by providing **RAMClustR** an experiment definition file. This file can be created manually or using the {% tool [RAMClustR define experiment](toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2) %} tool. There we can specify annotations such as what instrument we used or ionisation mode (which was EI+ in our case), and this will be transfered to the `.msp` file. Finally, we can provide such a file as an input to **RAMClustR** in the _Extras_ inputs section. -> > -> {: .details} +> Click *"View data"* {% icon galaxy-eye %} icon next to the dataset in the Galaxy history. The contents of the file would look like this: +> +> {% snippet faqs/galaxy/datasets_icons.md %} +> +> ``` +> NAME:C001 +> IONMODE:Negative +> SPECTRUMTYPE:Centroid +> RETENTIONTIME:383.27 +> Num Peaks:231 +> 217.1073 64041926 +> 243.0865 35597866 +> 257.1134 31831229 +> 224.061 27258239 +> 258.11 24996353 +> 241.0821 23957171 +> 315.1188 13756744 +> ... +> +> NAME:C002 +> IONMODE:Negative +> SPECTRUMTYPE:Centroid +> RETENTIONTIME:281.62 +> Num Peaks:165 +> 307.1573 299174880 +> 147.0654 298860831 +> 149.0447 287809889 +> 218.1066 118274758 +> 189.076 112486871 +> 364.1787 75134143 +> 191.0916 52526567 +> 308.1579 52057158 +> ... +> ``` +> +> > Negative ion mode +> > +> > You might wonder how can the ionisation mode (_IONMODE_) for GC-MS data be negative when using electron impact (EI+) ionization. This is, of course, incorrect. This is actually just a default behaviour of **RAMClustR**. We can optionally change this by providing **RAMClustR** an experiment definition file. This file can be created manually or using the {% tool [RAMClustR define experiment](toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2) %} tool. There we can specify annotations such as what instrument we used or ionisation mode (which was EI+ in our case), and this will be transfered to the `.msp` file. Finally, we can provide such a file as an input to **RAMClustR** in the _Extras_ inputs section. +> > +> {: .details} > {: .hands_on} diff --git a/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.md b/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.md index 00e8cc5e0a2116..5025fbdcc93fc6 100644 --- a/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.md +++ b/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.md @@ -68,7 +68,7 @@ The "Data Upload" process is the only one in this tutorial that takes place dire > Data upload > -> Import the FASTQ file pairs from [Zenodo]({{ page.zenodo_link }}) or a data library: +> 1. Import the FASTQ file pairs from [Zenodo]({{ page.zenodo_link }}) or a data library: > - `GSM461177` (untreated): `GSM461177_1` and `GSM461177_2` > - `GSM461180` (treated): `GSM461180_1` and `GSM461180_2` > @@ -79,9 +79,9 @@ The "Data Upload" process is the only one in this tutorial that takes place dire > {{ page.zenodo_link }}/files/GSM461180_2.fastqsanger > ``` > -> {% snippet faqs/galaxy/datasets_import_via_link.md %} +> 2. {% snippet faqs/galaxy/datasets_import_via_link.md %} > -> {% snippet faqs/galaxy/datasets_import_from_data_library.md %} +> 3. {% snippet faqs/galaxy/datasets_import_from_data_library.md %} > > > > > @@ -98,12 +98,11 @@ The "Data Upload" process is the only one in this tutorial that takes place dire > > > {: .comment} > -> Change the datatype from `fastqsanger` to `fastq`. +> 4. Change the datatype from `fastqsanger` to `fastq`. > > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="fastq" %} > -> -> We also need to import two more files, essential for the alignment operation (and basically every alignment procedure): the organism's reference genome (here *D. melanogaster*) and the organism's gene annotation. +> 5. We also need to import two more files, essential for the alignment operation (and basically every alignment procedure): the organism's reference genome (here *D. melanogaster*) and the organism's gene annotation. > Those can be aquired directly via link and Galaxy's data library as described above. For this tutorial we are going to use the files [dm6.fa.gz](https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz) and [Drosophila_melanogaster.BDGP6.87.gtf (dm6)](https://usegalaxy.eu/libraries/folders/F30cab321d898d2fb/dataset/02c5f7fcdb6bf41f). Note that it is essential to convert genome's file from `*.fa.gz` to `*.fa`. That is easy now that we have already used the same method to convert `fastqsanger` to `fastq`. Remember to change the name of the file, too, in your working history as Galaxy will not do it automatically. Doing so will prevent any confusions later on. > > {% snippet faqs/galaxy/datasets_rename.md name="dm6.fa" %} From 5d1003fa572e0efc5021847e5a405663c60e62df Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Sun, 9 Jul 2023 07:17:03 +0200 Subject: [PATCH 3/3] negate exit --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7b00a0e98c33f0..7ea5b8e005c73d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -73,7 +73,7 @@ jobs: - name: Ensure no unexpected encoded HTML in output run: | - fgrep -R 'lt;blockquote' _site + ! fgrep -R 'lt;blockquote' _site - name: Run aXe accessibility testing on some representative URLs run: |