From 8f8d8da9567cc297471ba1102f4514b24741c393 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 18 Jun 2024 01:15:35 +0200 Subject: [PATCH 01/63] fix copypasta --- topics/dev/tutorials/tool-from-scratch/tutorial.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/topics/dev/tutorials/tool-from-scratch/tutorial.md b/topics/dev/tutorials/tool-from-scratch/tutorial.md index 3bbcd56589aac7..4253ea92e2f529 100644 --- a/topics/dev/tutorials/tool-from-scratch/tutorial.md +++ b/topics/dev/tutorials/tool-from-scratch/tutorial.md @@ -433,8 +433,7 @@ anyone wrapping a tool, a more complete list is available in [the Galaxy tool do Planemo is an important tool within the Galaxy development workflow. Although it will be covered in greater detail in the next section of this tutorial, one of its functions is necessary for the tool wrapper development. `planemo` is available -via the python package manager `pip`. To that end, before beginning this section, please install `planemo` locally by running -`planemo`. To that end, before beginning this section, please install planemo locally by running +via the python package manager `pip`. To that end, before beginning this section, please install planemo locally by running > Installing `planemo` via pip > From 0505a774b2a297fece454ee22c6484bf721600a6 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 12 Sep 2024 11:52:51 +0000 Subject: [PATCH 02/63] add new recording from Google Form submission --- .../tutorials/scrna-case_alevin/tutorial.md | 95 +++++++++---------- 1 file changed, 45 insertions(+), 50 deletions(-) diff --git a/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md b/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md index d289b2d30693c0..4a168032bfb9bb 100644 --- a/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md +++ b/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md @@ -1,72 +1,56 @@ --- layout: tutorial_hands_on - -title: "Generating a single cell matrix using Alevin" +title: Generating a single cell matrix using Alevin subtopic: single-cell-CS priority: 1 - -zenodo_link: 'https://zenodo.org/record/4574153' - +zenodo_link: https://zenodo.org/record/4574153 redirect_from: -- /topics/transcriptomics/tutorials/droplet-quantification-preprocessing/tutorial -- /topics/transcriptomics/tutorials/scrna-case_alevin/tutorial - +- "/topics/transcriptomics/tutorials/droplet-quantification-preprocessing/tutorial" +- "/topics/transcriptomics/tutorials/scrna-case_alevin/tutorial" questions: - - I have some single cell FASTQ files I want to analyse. Where do I start? - +- I have some single cell FASTQ files I want to analyse. Where do I start? answer_histories: - - label: "UseGalaxy.eu" - history: https://usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-alevin - date: 2024-03-22 - - label: "Older Alevin version" - history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key - date: 2024-01-01 - +- label: UseGalaxy.eu + history: https://usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-alevin + date: 2024-03-22 +- label: Older Alevin version + history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key + date: 2024-01-01 input_histories: - - label: "UseGalaxy.eu" - history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1 - +- label: UseGalaxy.eu + history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1 objectives: - - Generate a cellxgene matrix for droplet-based single cell sequencing data - - Interpret quality control (QC) plots to make informed decisions on cell thresholds - - Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata - +- Generate a cellxgene matrix for droplet-based single cell sequencing data +- Interpret quality control (QC) plots to make informed decisions on cell thresholds +- Find relevant information in GTF files for the particulars of their study, and include + this in data matrix metadata time_estimation: 2H - key_points: - - Create a scanpy-accessible AnnData object from FASTQ files, including relevant gene metadata - +- Create a scanpy-accessible AnnData object from FASTQ files, including relevant gene + metadata tags: - - 10x - - paper-replication - +- 10x +- paper-replication contributions: authorship: - - nomadscientist - - pinin4fjords - + - nomadscientist + - pinin4fjords editing: - - hexylena - + - hexylena testing: - - wee-snufkin - + - wee-snufkin requirements: - - type: "internal" - topic_name: single-cell - tutorials: - - scrna-intro - - scrna-umis - +- type: internal + topic_name: single-cell + tutorials: + - scrna-intro + - scrna-umis gitter: Galaxy-Training-Network/galaxy-single-cell - follow_up_training: - - - type: "internal" - topic_name: single-cell - tutorials: - - scrna-case_alevin-combine-datasets - +- type: internal + topic_name: single-cell + tutorials: + - scrna-case_alevin-combine-datasets recordings: - captioners: - nomadscientist @@ -76,10 +60,21 @@ recordings: youtube_id: 3ytm2AU6QUc speakers: - nomadscientist +- youtube_id: TODO + length: 49M + galaxy_version: 24.1.2.dev0 + date: '2024-09-12' + speakers: + - MarisaJL + captioners: + - MarisaJL + bot-timestamp: 1726104172 + --- + This tutorial will take you from raw FASTQ files to a cell x gene data matrix in AnnData format. What's a data matrix, and what's AnnData format? Well you'll find out! Importantly, this is the first step in processing single cell data in order to start analysing it. Currently you have a bunch of strings of `ATGGGCTT` etc. in your sequencing files, and what you need to know is how many cells you have and what genes appear in those cells. These steps are the most computationally heavy in the single cell world, as you're starting with 100s of millions of reads, each with 4 lines of text. Later on in analysis, this data becomes simple gene counts such as 'Cell A has 4 GAPDHs', which is a lot easier to store! Because of this data overload, we have downsampled the FASTQ files to speed up the analysis a bit. Saying that, you're still having to map loads of reads to the massive murine genome, so get yourself a cup of coffee and prepare to analyse! > From 20a48db9beb3340fe78a7e69c9b7c6d0e722f739 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Fri, 13 Sep 2024 18:20:28 +0200 Subject: [PATCH 03/63] Update topics/single-cell/tutorials/scrna-case_alevin/tutorial.md --- topics/single-cell/tutorials/scrna-case_alevin/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md b/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md index 4a168032bfb9bb..05b6a5b2dcc5b5 100644 --- a/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md +++ b/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md @@ -60,7 +60,7 @@ recordings: youtube_id: 3ytm2AU6QUc speakers: - nomadscientist -- youtube_id: TODO +- youtube_id: BQriffof8yM length: 49M galaxy_version: 24.1.2.dev0 date: '2024-09-12' From 22d275105ce5ee20c5a4214d868e377683b2a17b Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Sun, 6 Oct 2024 10:44:05 +0000 Subject: [PATCH 04/63] add new recording from Google Form submission --- topics/statistics/tutorials/CNN/tutorial.md | 29 ++++++++++++++------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/topics/statistics/tutorials/CNN/tutorial.md b/topics/statistics/tutorials/CNN/tutorial.md index c9633eebe9d2ba..82a619b051b130 100644 --- a/topics/statistics/tutorials/CNN/tutorial.md +++ b/topics/statistics/tutorials/CNN/tutorial.md @@ -1,6 +1,5 @@ --- layout: tutorial_hands_on - title: Deep Learning (Part 3) - Convolutional neural networks (CNN) zenodo_link: https://zenodo.org/record/4697906 questions: @@ -10,19 +9,18 @@ objectives: - Understand the inspiration behind CNN and learn the CNN architecture - Learn the convolution operation and its parameters - Learn how to create a CNN using Galaxy's deep learning tools -- Solve an image classification problem on MNIST digit classification dataset using CNN in Galaxy +- Solve an image classification problem on MNIST digit classification dataset using + CNN in Galaxy requirements: - - - type: internal - topic_name: statistics - tutorials: - - intro_deep_learning - - FNN - - RNN +- type: internal + topic_name: statistics + tutorials: + - intro_deep_learning + - FNN + - RNN time_estimation: 2H contributors: - kxk302 - recordings: - captioners: - FilipposZ @@ -32,10 +30,21 @@ recordings: youtube_id: P1NVYOJrv_4 speakers: - kxk302 +- youtube_id: TODO + length: 45M + galaxy_version: " 24.1.3.dev0" + date: '2024-10-05' + speakers: + - hujambo-dunia + captioners: + - hujambo-dunia + bot-timestamp: 1728137291 + --- + Artificial neural networks are a machine learning discipline that have been successfully applied to problems in pattern classification, clustering, regression, association, time series prediction, optimiztion, and control {% cite JainEtAl %}. With the increasing popularity of social media in the past decade, image and video processing tasks have become very From b9def62af03d2b50063f1a29c391a1368609b32c Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Sun, 6 Oct 2024 09:25:42 -0400 Subject: [PATCH 05/63] add youtube id --- topics/statistics/tutorials/CNN/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/statistics/tutorials/CNN/tutorial.md b/topics/statistics/tutorials/CNN/tutorial.md index 82a619b051b130..c34db830f38f48 100644 --- a/topics/statistics/tutorials/CNN/tutorial.md +++ b/topics/statistics/tutorials/CNN/tutorial.md @@ -30,7 +30,7 @@ recordings: youtube_id: P1NVYOJrv_4 speakers: - kxk302 -- youtube_id: TODO +- youtube_id: 1EbW7Eec9FQ length: 45M galaxy_version: " 24.1.3.dev0" date: '2024-10-05' From 1650c75a3c5e3c2aff6bff07678df5ed64f08951 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Sun, 6 Oct 2024 16:39:12 -0400 Subject: [PATCH 06/63] Update to the latest version of the video --- topics/statistics/tutorials/CNN/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/statistics/tutorials/CNN/tutorial.md b/topics/statistics/tutorials/CNN/tutorial.md index c34db830f38f48..9a2dcfaea56234 100644 --- a/topics/statistics/tutorials/CNN/tutorial.md +++ b/topics/statistics/tutorials/CNN/tutorial.md @@ -30,7 +30,7 @@ recordings: youtube_id: P1NVYOJrv_4 speakers: - kxk302 -- youtube_id: 1EbW7Eec9FQ +- youtube_id: vp6YF2NRIZk length: 45M galaxy_version: " 24.1.3.dev0" date: '2024-10-05' From e4a98f5870a7569e8460f328adfd8e78174799aa Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Mon, 7 Oct 2024 07:47:44 +0000 Subject: [PATCH 07/63] add new recording from Google Form submission --- .../ERGA-post-assembly-QC/tutorial.md | 41 +++++++++++++------ 1 file changed, 28 insertions(+), 13 deletions(-) diff --git a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md index c1eb9cb8a9aa85..e49c8f96e32bf2 100644 --- a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md +++ b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md @@ -1,30 +1,45 @@ --- layout: tutorial_hands_on - title: ERGA post-assembly QC questions: -- "What combination of tools can assess the quality of a genome assembly?" -- "What metrics can help to analyse the quality of an asembly?" -- "How do we evaluate the outputs?" +- What combination of tools can assess the quality of a genome assembly? +- What metrics can help to analyse the quality of an asembly? +- How do we evaluate the outputs? objectives: -- "Apply the post-assembly-QC-workflow using the necessary tools" -- "Analyse and evaluate the results of the workflow" +- Apply the post-assembly-QC-workflow using the necessary tools +- Analyse and evaluate the results of the workflow time_estimation: 3H key_points: -- "The ERGA post-assembly pipeline allows users to assess and improve the quality of genome assemblies" -- "The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics, and Hi-C scaffolding." +- The ERGA post-assembly pipeline allows users to assess and improve the quality of + genome assemblies +- 'The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination + and overview with BlobToolKit, providing analysis information and statistics, and + Hi-C scaffolding.' contributors: - GitFab93 - gallardoalba - tbrown91 tags: - - plants - - animals - - genome - - assembly - - QC +- plants +- animals +- genome +- assembly +- QC +recordings: +- youtube_id: TODO + length: 44M + galaxy_version: 24.1.3.dev0 + date: '2024-10-06' + speakers: + - delphine-l + captioners: + - delphine-l + bot-timestamp: 1728229662 + + --- + ![ERGA logo, 4 colorful letters on white background, with the European star circle](../../images/post-assembly-QC/ERGA.logo.jpg){: width="20px"} The European Reference Genome Atlas ([ERGA](https://www.erga-biodiversity.eu/), {% cite Mazzoni2023 %}) is a large-scale network of researchers aiming to generate high-quality reference genomes for all eukaryotic life in Europe and build capacity to allow researchers anywhere to generate reference genomes and use them to answer questions regarding species conservation and biodiversity. ERGA uses state-of-the-art sequencing technologies and advanced bioinformatics tools to produce high-quality genome assemblies. From 8a1b9bf451014b4074330d629ac37c1f171c62f3 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Mon, 7 Oct 2024 12:24:59 +0200 Subject: [PATCH 08/63] Update topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md --- topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md index e49c8f96e32bf2..29c5539513bf5e 100644 --- a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md +++ b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md @@ -26,7 +26,7 @@ tags: - assembly - QC recordings: -- youtube_id: TODO +- youtube_id: n4PNTTa2d6U length: 44M galaxy_version: 24.1.3.dev0 date: '2024-10-06' From 412ee1eeefea32c1a4f019b2548bf03886203c22 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Mon, 7 Oct 2024 21:51:46 +0200 Subject: [PATCH 09/63] Update topics/statistics/tutorials/CNN/tutorial.md --- topics/statistics/tutorials/CNN/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/statistics/tutorials/CNN/tutorial.md b/topics/statistics/tutorials/CNN/tutorial.md index 9a2dcfaea56234..b215d4584024ff 100644 --- a/topics/statistics/tutorials/CNN/tutorial.md +++ b/topics/statistics/tutorials/CNN/tutorial.md @@ -32,7 +32,7 @@ recordings: - kxk302 - youtube_id: vp6YF2NRIZk length: 45M - galaxy_version: " 24.1.3.dev0" + galaxy_version: 24.1.3.dev0 date: '2024-10-05' speakers: - hujambo-dunia From 68773b35f82468030143cbd0a4476b6ce324a751 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2024 10:50:14 +0200 Subject: [PATCH 10/63] Optimistically handle plausible button --- _layouts/tutorial_hands_on.html | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html index 7573628cd1d611..ae38499d40d824 100644 --- a/_layouts/tutorial_hands_on.html +++ b/_layouts/tutorial_hands_on.html @@ -290,10 +290,13 @@

You've Finished the Tutorial