From 5bb7e0f1503551ab461d0fe3f150d15fe757b0a8 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 13 Feb 2024 11:58:22 +0100 Subject: [PATCH] fix instance listing --- _layouts/workflow-list.html | 2 +- faqs/gtn/contributors_getting_started.md | 2 +- faqs/gtn/contributors_tours.md | 2 +- short/galaxy.html | 4 ++-- topics/admin/tutorials/introduction/slides.html | 2 +- topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.md | 2 +- topics/introduction/tutorials/galaxy-intro-short/slides.html | 2 +- .../tutorials/galaxy-intro-short/slides_CAT_ES.html | 2 +- topics/introduction/tutorials/galaxy-reproduce/tutorial.md | 2 +- topics/teaching/tutorials/workshop-intro/slides.html | 2 +- .../tutorials/rna-seq-reads-to-counts/tutorial.md | 2 +- 11 files changed, 12 insertions(+), 12 deletions(-) diff --git a/_layouts/workflow-list.html b/_layouts/workflow-list.html index 6ba7d4de7cdef0..b5a1e5732fa54e 100644 --- a/_layouts/workflow-list.html +++ b/_layouts/workflow-list.html @@ -48,7 +48,7 @@
Download Galaxy Workflow.ga - {% assign servers = list_usegalaxy_servers_shuffle %} + {% assign servers = nil | list_usegalaxy_servers_shuffle %} {% for server in servers %} {{ server.human }} {% endfor %} diff --git a/faqs/gtn/contributors_getting_started.md b/faqs/gtn/contributors_getting_started.md index 654517fd7aa3bc..3e06b1a29b351b 100644 --- a/faqs/gtn/contributors_getting_started.md +++ b/faqs/gtn/contributors_getting_started.md @@ -15,7 +15,7 @@ Below is a checklist of things to look out for to help you get started. If you f Basic: - **Test** the tutorial on a running Galaxy instance - - For example {% assign servers = list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %} + - For example {% assign servers = nil | list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %} - Report any issues you run into - **Language** editing - Fix spelling and grammar mistakes diff --git a/faqs/gtn/contributors_tours.md b/faqs/gtn/contributors_tours.md index daee90427075fb..2e25719a749ec1 100644 --- a/faqs/gtn/contributors_tours.md +++ b/faqs/gtn/contributors_tours.md @@ -9,7 +9,7 @@ contributors: [shiltemann] Perhaps you've been asked to review an interactive tour, or maybe you just want to try one out. The easiest way to run an interactive tour is to use the [Tour builder](https://tailordev.fr/blog/2017/07/19/the-galaxy-tour-builder-extension/) browser extension. 1. Install the Tour Builder extension to your browser ([Chrome Web Store](https://chrome.google.com/webstore/detail/galaxy-tour-builder/mdfbapknmcpnbmggahhaegehbbbmhmgg), [Firefox add-on](https://addons.mozilla.org/en-US/firefox/addon/galaxy-tour-builder/)). -2. Navigate to a Galaxy instance supporting the tutorial. To find which Galaxy instances support each tutorial, please see the dropdown menu next to the tutorial on the training website. Using one of the usegalaxy.\* instances ({% assign servers = list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}) +2. Navigate to a Galaxy instance supporting the tutorial. To find which Galaxy instances support each tutorial, please see the dropdown menu next to the tutorial on the training website. Using one of the usegalaxy.\* instances ({% assign servers = nil | list_usegalaxy_servers_shuffle %}{% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}) ) is usually a good bet. 3. Start the Tour Builder plugin by clicking on the icon in your browser menu bar 4. Copy the contents of the `tour.yaml` file into the Tour builder editor window diff --git a/short/galaxy.html b/short/galaxy.html index dfc434e88dfca5..e0fe33d55dbd94 100644 --- a/short/galaxy.html +++ b/short/galaxy.html @@ -5,7 +5,7 @@ ---
-
+

My Galaxy Training

@@ -25,7 +25,7 @@

Go!

Select your Preferred Galaxy Server

- {% assign servers = list_usegalaxy_servers_shuffle %} + {% assign servers = nil | list_usegalaxy_servers_shuffle %} {% for server in servers %} {{ server.human }} ({{ server.id | upcase }}) {% endfor %} diff --git a/topics/admin/tutorials/introduction/slides.html b/topics/admin/tutorials/introduction/slides.html index fdd9a63a6f419d..20155804546324 100644 --- a/topics/admin/tutorials/introduction/slides.html +++ b/topics/admin/tutorials/introduction/slides.html @@ -33,7 +33,7 @@ # Where can Galaxy run? -{% assign servers = list_usegalaxy_servers_shuffle %} +{% assign servers = nil | list_usegalaxy_servers_shuffle %} * Cloud (SaaS) - A usegalaxy.* site: {% for server in servers %}[{{ server.human }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %} diff --git a/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.md b/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.md index 2e25fbca2f6997..d4a772eb1ba221 100644 --- a/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.md +++ b/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.md @@ -104,7 +104,7 @@ We will import the JSON files into Galaxy to query them directory, however the f > {: .comment} -{% assign servers = list_usegalaxy_servers_shuffle %} +{% assign servers = nil | list_usegalaxy_servers_shuffle %} > Loading SRA Aligned Read Format (SARF) Object Metadata URLs into Galaxy > diff --git a/topics/introduction/tutorials/galaxy-intro-short/slides.html b/topics/introduction/tutorials/galaxy-intro-short/slides.html index 3fa21260fd0a1a..12d6b5f1503be4 100644 --- a/topics/introduction/tutorials/galaxy-intro-short/slides.html +++ b/topics/introduction/tutorials/galaxy-intro-short/slides.html @@ -101,7 +101,7 @@ # Find a Galaxy server -{% assign servers = list_usegalaxy_servers_shuffle %} +{% assign servers = nil | list_usegalaxy_servers_shuffle %} - **UseGalaxy.\***: {% for server in servers %}{{ server.human }} ([{{ server.name }}]({{ server.url }})){% if forloop.last %}{% else %}, {% endif %}{% endfor %} .image-50[![usegalaxy.* servers]({{site.baseurl}}/shared/images/usegalaxy_servers.png)] diff --git a/topics/introduction/tutorials/galaxy-intro-short/slides_CAT_ES.html b/topics/introduction/tutorials/galaxy-intro-short/slides_CAT_ES.html index 4c78d3ffbaf491..52290a61098105 100644 --- a/topics/introduction/tutorials/galaxy-intro-short/slides_CAT_ES.html +++ b/topics/introduction/tutorials/galaxy-intro-short/slides_CAT_ES.html @@ -108,7 +108,7 @@ # Encuentra un servidor Galaxy -{% assign servers = list_usegalaxy_servers_shuffle %} +{% assign servers = nil | list_usegalaxy_servers_shuffle %} - ** Los tres grandes **: {% for server in servers %}{{ server.human }} ([{{ server.name }}]({{ server.url }})){% if forloop.last %}{% else %}, {% endif %}{% endfor %} .image-75[![usegalaxy.* servidores]({{site.baseurl}}/shared/images/usegalaxy_servers.png)] diff --git a/topics/introduction/tutorials/galaxy-reproduce/tutorial.md b/topics/introduction/tutorials/galaxy-reproduce/tutorial.md index 6f527dab87a60b..28cdd51fd20c04 100644 --- a/topics/introduction/tutorials/galaxy-reproduce/tutorial.md +++ b/topics/introduction/tutorials/galaxy-reproduce/tutorial.md @@ -40,7 +40,7 @@ For more background information about Galaxy, have a look into the Galaxy public # What does Galaxy look like? -{% assign servers = list_usegalaxy_servers_shuffle %} +{% assign servers = nil | list_usegalaxy_servers_shuffle %} Many different Galaxy servers exist. Some are public, some are private, some focus on a specific topic and others like the usegalaxy.\* servers cover a broad range of tools. To reproduce published results it is highly recommended to use the same Galaxy server that was used in the original study. In the case that this was a private server that is not accessible to you, you might want to use one of the main Galaxy servers: {% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}. To learn more about the different Galaxy servers visit the [slides: options for using Galaxy]({% link /topics/introduction/tutorials/options-for-using-galaxy/slides.html %}). The particular Galaxy server that you are using may look slightly different than the one shown in this training. Galaxy instance administrators can choose the exact version of Galaxy they would like to offer and can customize its look to some extent. The basic functionality will be rather similar across instances, so don’t worry! In this training we will use the European Galaxy server on which the original analysis was performed and shared. diff --git a/topics/teaching/tutorials/workshop-intro/slides.html b/topics/teaching/tutorials/workshop-intro/slides.html index f0b783cb8a58f0..20699862d6eab5 100644 --- a/topics/teaching/tutorials/workshop-intro/slides.html +++ b/topics/teaching/tutorials/workshop-intro/slides.html @@ -245,7 +245,7 @@ - Training materials: https://training.galaxyproject.org - Galaxy (an instructor will tell you which Galaxy to use) - {% assign servers = list_usegalaxy_servers_shuffle %} + {% assign servers = nil | list_usegalaxy_servers_shuffle %} {% for server in servers %} - {{ server.name }} {{ server.url }} {% endfor %} diff --git a/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.md b/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.md index 3482ca87d75592..ffdcffb0059d00 100644 --- a/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.md +++ b/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.md @@ -82,7 +82,7 @@ This is a Galaxy tutorial based on material from the [COMBINE R RNAseq workshop] ## Import data from URLs -{% assign servers = list_usegalaxy_servers_shuffle %} +{% assign servers = nil | list_usegalaxy_servers_shuffle %} Read sequences are usually stored in compressed (gzipped) FASTQ files. Before the differential expression analysis can proceed, these reads must be aligned to the reference genome and counted into annotated genes. Mapping reads to the genome is a very important task, and many different aligners are available, such as HISAT2 ({% cite kim2015hisat %}), STAR ({% cite dobin2013star %}) and Subread ({% cite Liao2013 %}). Most mapping tasks require larger computers than an average laptop, so usually read mapping is done on a server in a linux-like environment, requiring some programming knowledge. However, Galaxy enables you to do this mapping without needing to know programming and if you don't have access to a server you can try to use one of the publically available Galaxies e.g. {% for server in servers %}[{{ server.name }}]({{ server.url }}){% if forloop.last %}{% else %}, {% endif %}{% endfor %}.