diff --git a/topics/admin/tutorials/interactive-tools/tutorial.md b/topics/admin/tutorials/interactive-tools/tutorial.md index 001ad515ecdfe4..fc616f0e836aa0 100644 --- a/topics/admin/tutorials/interactive-tools/tutorial.md +++ b/topics/admin/tutorials/interactive-tools/tutorial.md @@ -36,15 +36,13 @@ requirements: subtopic: features --- + +Galaxy Interactive Tools (GxITs) are a method to run containerized tools that are interactive in nature. Interactive Tools typically run a persistent service accessed on a specific port and run until terminated by the user. One common example of such a tool is [Jupyter Notebook][jupyter]. Galaxy Interactive Tools are similar in purpose to [Galaxy Interactive Environments][gie-docs] (GIEs), but are implemented in a significantly different manner. Most notably, instead of directly invoking containers on the Galaxy server, dedicated Docker node, or as a Docker Swarm service (as is done for GIEs), Interactive Tools are submitted through Galaxy's job management system and thus are scheduled the same as any other Galaxy tool - on a Slurm cluster, for instance. Galaxy Interactive Tools were introduced in Galaxy Release 19.09. + > Evolving Topic, Not Updated for 23.0 + Gravity > Galaxy Interactive Tools are a **new feature** and there are some rough edges. Work to improve the experience of deploying and using them is ongoing. {: .warning} -# Overview - - -Galaxy Interactive Tools (GxITs) are a method to run containerized tools that are interactive in nature. Interactive Tools typically run a persistent service accessed on a specific port and run until terminated by the user. One common example of such a tool is [Jupyter Notebook][jupyter]. Galaxy Interactive Tools are similar in purpose to [Galaxy Interactive Environments][gie-docs] (GIEs), but are implemented in a significantly different manner. Most notably, instead of directly invoking containers on the Galaxy server, dedicated Docker node, or as a Docker Swarm service (as is done for GIEs), Interactive Tools are submitted through Galaxy's job management system and thus are scheduled the same as any other Galaxy tool - on a Slurm cluster, for instance. Galaxy Interactive Tools were introduced in Galaxy Release 19.09. - > Before You Continue > If you are *not* completing this tutorial as part of a [Galaxy Admin Training][gat] course, **you will need a wildcard DNS record for your Galaxy server and a method for obtaining a wildcard SSL certificate for your Galaxy server**. > diff --git a/topics/data-science/tutorials/git-cli/tutorial.md b/topics/data-science/tutorials/git-cli/tutorial.md index 2345958a18397e..2f837126124509 100644 --- a/topics/data-science/tutorials/git-cli/tutorial.md +++ b/topics/data-science/tutorials/git-cli/tutorial.md @@ -27,12 +27,12 @@ requirements: - cli-basics --- +Version control is a way of tracking the change history of a project. Even if you have never used a version control tool, you've probably already done it manually: copying and renaming project folders ("paper-1.doc", "paper-2.doc", etc.) is a form of version control. Within bioinformatics (from research, to development, to sysadmin) a lot of us are using `git` as our primary method of source control for everything we do: notes, slides, tutorials, code, notebooks, ansible, system configuration, and more. + > Source > This tutorial contains text from [this tutorial](https://github.com/rdadolf/git-tutorial/) by Robert Adolf ([@rdadolf](https://github.com/rdadolf)), which is licensed CC-BY. {: .comment} -Version control is a way of tracking the change history of a project. Even if you have never used a version control tool, you've probably already done it manually: copying and renaming project folders ("paper-1.doc", "paper-2.doc", etc.) is a form of version control. Within bioinformatics (from research, to development, to sysadmin) a lot of us are using `git` as our primary method of source control for everything we do: notes, slides, tutorials, code, notebooks, ansible, system configuration, and more. - Git is a tool that automates and enhances a lot of the tasks that arise when dealing with larger, longer-living, and collaborative projects. It's also become the common underpinning to many popular online code repositories, GitHub being the most popular. While it can be used collaboratively, this tutorial focuses on a single-user git repository for the most basic operations. diff --git a/topics/data-science/tutorials/python-multiprocessing/tutorial.md b/topics/data-science/tutorials/python-multiprocessing/tutorial.md index 55fba7ed348827..ec8e396d455062 100644 --- a/topics/data-science/tutorials/python-multiprocessing/tutorial.md +++ b/topics/data-science/tutorials/python-multiprocessing/tutorial.md @@ -36,6 +36,9 @@ abbreviations: GIL: Global Interpreter Lock --- +This tutorial will introduce you to the basics of Threads and Processes in +Python and how you can use them to parallelise your code. + > > diff --git a/topics/data-science/tutorials/sql-basic/tutorial.md b/topics/data-science/tutorials/sql-basic/tutorial.md index 337bf63e2b267b..961f32233ebfe2 100644 --- a/topics/data-science/tutorials/sql-basic/tutorial.md +++ b/topics/data-science/tutorials/sql-basic/tutorial.md @@ -70,6 +70,8 @@ tags: - SQL --- +This tutorial will introduce you to {SQL} which can be used to query databases! + > > > This tutorial is **significantly** based on [the Carpentries](https://carpentries.org) [Databases and SQL](https://github.com/swcarpentry/sql-novice-survey/) lesson, which is licensed CC-BY 4.0. diff --git a/topics/data-science/tutorials/sql-python/tutorial.md b/topics/data-science/tutorials/sql-python/tutorial.md index a999108558f5b0..5fc3859c797cc9 100644 --- a/topics/data-science/tutorials/sql-python/tutorial.md +++ b/topics/data-science/tutorials/sql-python/tutorial.md @@ -40,6 +40,8 @@ tags: - Python --- +This tutorial will introduce you to accessing a SQL database from within Python. Experience with both SQL and Python is a pre-requisite. + > > > This tutorial is **significantly** based on [the Carpentries](https://carpentries.org) [Databases and SQL](https://github.com/swcarpentry/sql-novice-survey/) lesson, which is licensed CC-BY 4.0. diff --git a/topics/data-science/tutorials/sql-r/tutorial.md b/topics/data-science/tutorials/sql-r/tutorial.md index 1e90c7ee930ffe..425b2077449fee 100644 --- a/topics/data-science/tutorials/sql-r/tutorial.md +++ b/topics/data-science/tutorials/sql-r/tutorial.md @@ -45,6 +45,8 @@ tags: - R --- +In this tutorial you'll learn to use SQL via R. Some R and SQL experience is a pre-requisite. + > > > This tutorial is **significantly** based on [the Carpentries](https://carpentries.org) [Databases and SQL](https://github.com/swcarpentry/sql-novice-survey/) lesson, which is licensed CC-BY 4.0. diff --git a/topics/dev/tutorials/bioblend-api/tutorial.md b/topics/dev/tutorials/bioblend-api/tutorial.md index 6f0d30086104a9..08b70557621a97 100644 --- a/topics/dev/tutorials/bioblend-api/tutorial.md +++ b/topics/dev/tutorials/bioblend-api/tutorial.md @@ -33,7 +33,7 @@ notebook: #pyolite: true # Not possible due to https://pyodide.org/en/stable/project/roadmap.html#write-http-client-in-terms-of-web-apis --- - +BioBlend ({% cite Sloggett2013 %}) is a Python library to enable simple interaction with Galaxy ({% cite Afgan2018 %}) via the command line or scripts. > > diff --git a/topics/galaxy-interface/tutorials/search/tutorial.md b/topics/galaxy-interface/tutorials/search/tutorial.md index c0ca8d1fe31602..b0b395c5311aed 100644 --- a/topics/galaxy-interface/tutorials/search/tutorial.md +++ b/topics/galaxy-interface/tutorials/search/tutorial.md @@ -20,13 +20,4 @@ contributors: subtopic: histories --- -> -> -> In this tutorial, we will deal with: -> -> 1. TOC -> {:toc} -> -{: .agenda} - {% include topics/galaxy-interface/tutorials/search/search.md %}