name: inverse layout: true class: center, middle, inverse <div class="my-footer"><span> <img src="/training-material-dev/assets/images/CPT-60px.png" alt="Galaxy Training Network" style="height: 40px;"/> </span></div> --- # Introduction to Galaxy --- # What is Galaxy? --- [](https://galaxyproject.org/) - **Web-based** platform for computational biomedical research - Developed at Penn State, Johns Hopkins, OHSU and Cleveland Clinic with substantial outside contributions - **Open source** under [Academic Free License](https://opensource.org/licenses/AFL-3.0) - More than 5,300 [citations](https://www.zotero.org/groups/1732893/galaxy) - More than 80 [public Galaxy servers](https://galaxyproject.org/public-galaxy-servers/) - Many more non-public - Both general-purpose and domain-specific ??? - The Galaxy Team is composed by bioinformaticians and software engineers - OHSU = Oregon Health & Science University --- ### Core values - **Accessibility** - Users without programming experience can easily upload/retrieve data, run complex tools and workflows, and visualize data - **Reproducibility** - Galaxy captures information so that any user can understand and repeat a complete computational analysis - **Transparency** - Users can share or publish their analyses (histories, workflows, visualizations) - Pages: online Methods for your paper Pages: interactive, web-based documents that describe a complete analysis. ??? **accessible** **reproducible** **transparent** research means <i>sharing everything</i>. If the Galaxy framework makes everything as simple as possible, researchers are able to: - share their analyses - track all used tools and versions - check all parameters - justify each step in the analysis - publish the findings with all aforementioned information --- # User Interface --- ### Main Galaxy interface  Home page divided into 3 panels --- ### Top menu  - *Analyze Data* - go back to the 3-panels homepage - *Workflow* - access existing workflows or create new one using the editable diagrammatic pipeline - *Shared data* - access data libraries, histories, workflows, visualizations and pages shared with you - *Visualization* - create new track browser and access your saved visualisations - *Help* - links to Galaxy Biostar (Q&A), Galaxy Community Hub (Wiki), and Interactive Tours - *User* – your preferences and saved histories, datasets, and pages --- ### Tool interface  --- ### Tools - Each tool is a text file describing: - input datasets, parameters, commands, and outputs - help, tests, citations, dependency requirements - Free tool store: [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/) - Thousands of tools already available - Every software can be embedded - If a tool is not available, ask the Galaxy community for help! - Only a Galaxy admin can install tools - New versions can be installed without removing old ones to ensure reproducibility ??? A tool describes: - the input datasets and their datatypes - the tool parameters (numerical, text, boolean, selections, colour) - how to generate a command to execute the tool with the specified inputs and parameters - the output datasets the tool should produce and their datatypes Tools can be viewed as tiny LEGO pieces: each one solves a specific problem, and they can be combined together to build complex analysis pipelines. --- ### History - Location of all your analyses <img style="float: right;" alt="History" src="../images/history.png" /> - collects all datasets produced by tools you run - collects all operations performed on your data - At the heart of Galaxy’s reproducibility<br /> For each dataset, the history tracks: - name, format, size, creation time, datatype-specific metadata - tool id and version, inputs, parameters - standard output (`stdout`) and error (`stderr`) - state (<span style="background-color: grey">waiting</span>, <span style="background-color: yellow">running</span>, <span style="background-color: green">success</span>, <span style="background-color: red">failed</span>) - hidden, deleted, purged ??? We say <i>datasets</i> to refer to files as well as databases Purged means permanently deleted --- ### Multiple histories - You can have as many histories as you want - each history should correspond to a **different analysis** - and should have a meaningful **name** --- ### History options menu - History behavior is controlled by the *History options* (gear icon) <img style="float: right;" alt="History menu" src="../images/galaxy_interface_history_long_menu.png" /> .image-25[] - *Create New* history will **not** make your current history disappear - To list all your histories, choose *Saved Histories* - You can *Copy Datasets* from one history to another - saves disk space and your quota --- # Loading data --- ### Importing data - Copy/paste from a file - Upload data from a local computer - Upload data from internet - Upload data from online databases - UCSC, BioMart, ENCODE, modENCODE, Flymine etc. - Import from Shared Data (libraries, histories, pages) - Upload data from FTP (>2GB) See [Getting data into Galaxy](../tutorials/galaxy-intro-get-data/slides.html) --- ### Datatypes - When uploading, datatype can be automatically detected or assigned by user - For datasets produced by a tool, the datatype is assigned by the tool - Tools only accept input datasets with the appropriate datatypes - You can change the datatype of a dataset in 2 ways: - Edit Attributes -> Datatype - Edit Attributes -> Convert Formats ??? - Edit Attributes -> Datatype is used to fix a wrongly assigned datatype - Edit Attributes -> Convert Formats creates a new dataset using a tool that converts the original dataset in the new format - New datatypes can be added to the Galaxy code base, if missing --- ### Reference genomes - Genome build specifies which genome assembly a dataset is associated with - e.g. mm10, hg38... - Genome build can be automatically detected or assigned by user - User can define their own custom genome build - New genome assemblies can be added by the site Galaxy admin --- # Workflows --- ### Workflow interface  ??? - Boxes are workflow steps - 2 types: *input* and *tool* steps - Steps are connected by arrows representing the flow of datasets - Tool panel on the left with Inputs on top (to add input datasets and collections) - Small tool form on the right --- ### Workflows - Can be **extracted** from a history - Allow to easily convert an existing history into an analysis workflow - Can be **built manually** by adding and configuring tools using the workflow canvas - Can be **imported** using an existing shared workflow --- ### Why would you want to create workflows? - **Re-run** the same analysis on different input data sets - **Change parameters** before re-running a similar analysis - Make use of the workflow job **scheduling** - jobs are submitted as soon as their inputs are ready - Create **sub**-workflows: a workflow inside another workflow - **Share** workflows for publication and with the community --- ### Data sharing - You can share your Galaxy items - histories, workflows, visualizations, and pages - with other people in three different ways: - Directly using a Galaxy account's email addresses on the same instance - Using a web link, with anyone who knows the link - Using a web link and publishing it to make it accessible to everyone from the *Shared Data* menu - Tools are shared using the free tool store: [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/) --- ### Data visualization - Charts - Each datatype can have some visualizations associated - Track browser called Trackster - To visualize genomic data in a tightly integrated way --- ### Community - Be part of an active and friendly community - Get support and your questions answered on [Galaxy Biostars](https://biostar.usegalaxy.org/) - Access community curated documentation on [Galaxy Community Hub](https://www.galaxyproject.org/) - Learn more about Galaxy for scientists and for developers and admins on [Galaxy Training Community](https://cpt.tamu.edu/training-material-dev///training-material-dev) --- ## Related tutorials --- ## Thank you! This material is the result of a collaborative work. Thanks the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors (Andrea Bagnacani, Bérénice Batut, Saskia Hiltemann, Anne Pajon, Nicola Soranzo) ! <img src="/training-material-dev/assets/images/CPT.png" alt="Galaxy Training Network" style="height: 100px;"/> .footnote[Found a typo? Something is wrong in this tutorial? <br/>Edit it on [GitHub](https://github.com/TAMU-CPT/training-material/tree/master/topics/introduction/slides/introduction.html)]