.. _galaxy:

Galaxy
======
.. figure:: images/galaxyLogo.jpeg
    :width: 50%

`Galaxy <https://usegalaxy.org/>`_ is an open-source web application built for
scientific analyses featuring a public server located within the cloud,
accessible open-source software packages, custom Galaxy tools (Galaxy
ToolShed), and a user-friendly drag-and-drop interface. The platform is easy to
learn, requiring no programming experience, and used to build reproducible
bioinformatics workflows. Galaxy's community also serves as one of the few
active forums for bioinformaticians to collaborate, with over 150 active
members monthly.

Multiple tools are available to the user, including popular ones such as FastQC
(quality control), Bowtie2 (aligner), featureCounts (count reads in genes), and
many more. Galaxy's built-in drag-and-drop workflow also serves as
a transparent way to quickly communicate analyses to other researchers and
collaborators.

Galaxy is great for genomic analyses, especially for beginners or users without
lots of computational experience. Overall, it's one of the few cloud-based
community hubs for bioinformaticians of all skill-levels. The Galaxy community
is only getting stronger - with over 124,000 registered users since its
inception in 2007 and over 2000 GalaxyHelp members total.

.. figure:: images/galaxyBulkRNASeqWF.png

    The Galaxy UI. The lefthand sidebar shows the tools available to the user.
    The center features a workflow for Bulk RNASeq. The righthand sidebar shows
    additional information.


Getting Started with Galaxy
---------------------------
Utilize the `Galaxy
Training pages <https://training.galaxyproject.org/training-material/>`_ to
understand what workflows are possible for Galaxy and a specific workflow is
the `Bulk RNA Seq Analysis
<https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#data-upload>`_
Galaxy tutorial

Benefits
--------

1. **Easy to use** A drag-and-drop interface allows users to quickly understand
   where the data is located and what is happening every step of the workflow.
   This helps really helps both those who are in and outside of the lab.
   Anybody can quickly understand the input and output of a workflow.

2. **Cloud-based server** This enables bioinformaticians to quickly save and
   store information without the fear of it being lost on some random
   computer's filesystem or stored on an accidentally corrupted USB. Workflows
   and stored data can be shared via URL links.

3. **Many tools available** The bioinformatics field constantly pushes out
   novel tools, but at a rate that might be too difficult to keep up with.
   Galaxy's tools provides an easy search function to find these tools at their
   most up-to-date version. A bioinformatician who previously was unaware of
   a tool might discover it and realize it's a much better implementation, thus
   improving their workflow's analysis. This is a great way for people to
   distribute their tools and have people actually use them.

4. **Galaxy's training docs are well maintained and applicable** The Galaxy
   community shines in making training for applied projects. The documents are
   interactive, often featuring video, slides, transcript, written tutorial,
   etc. The training documents provide a great way to understand the extent
   that Galaxy can help with your project.

5. **Galaxy is constantly being updated to be more user-friendly and advanced**
   Not only does it have workflow management, Galaxy also boasts many tools for
   data visualization and even a Jupyter Notebook feature.

Drawbacks
---------
1. **Possible lack of customization** Some tools may not include all options
   that the tool would offer if manually installed. For example, "Operate on
   Genomic Intervals:Intersect" and "BED:bedtools Intersect intervals" are the
   same tool in Galaxy yet the command line ``bedtools`` offers more
   options. However, this is constantly being improved.

2. **Documentation** Some tools only have a link to the tool's
   original documentation.

3. **Name of Tools** The naming of the tools splits between Galaxy-programmed
   tools and Galaxy-adapted tools created by other pre-existing packages.
   For example, in the "Get Data" tab, there are two
   options to get data from NCBI SRA that look very similar: "Faster Download
   and Extract Reads in FASTQ" and "Download and Extract Reads in FASTA/Q".

Papers
------
`The Galaxy platform for accessible, reproducible and
collaborative biomedical analyses: 2018 update (Afghan, et al. 2018)
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030816/>`_