diff --git a/_layouts/workflow-list.html b/_layouts/workflow-list.html index 6ba7d4de7cdef..b5a1e5732fa54 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 654517fd7aa3b..3e06b1a29b351 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 daee90427075f..2e25719a749ec 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 dfc434e88dfca..e0fe33d55dbd9 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 fdd9a63a6f419..2015580454632 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 2e25fbca2f699..d4a772eb1ba22 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 3fa21260fd0a1..12d6b5f1503be 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 4c78d3ffbaf49..52290a6109810 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 6f527dab87a60..28cdd51fd20c0 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 f0b783cb8a58f..20699862d6eab 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 3482ca87d7559..ffdcffb0059d0 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 %}.