Atoms

This repository contains the de.STAIR atoms that are incorporated in the Galaxy workflow generator, to assist users in the analysis of RNA-Seq and BS/RRBS-Seq data.

• How it works
• Contributed atoms
  • DGE analysis (single-end reads)
  • DGE analysis (paired-end reads)
  • RRBS/BS-Seq analysis (paired-end reads)
• How to contribute
  • Set up Docker
  • When some tools are missing
  • When every tool is there
  • Test new atoms

How it works

Atoms are interactive Galaxy tours that illustrate one or more tools within the context of an experimental setup.
Alternative atoms are therefore provided to describe the usage and parameterization of alternative tools to solve the same biocomputational problem.

In the Galaxy workflow generator, each atom describes a tool (or series thereof) to solve a task of the desired data analysis.

For instance, to carry out the tasks of an RNA-Seq analysis:

1. Quality control and data preprocessing
2. Genome alignment
3. Transcript quantification and differential gene expression

alternative atoms can be built using the following Galaxy tools:

Where ^X,Y,Z,W are alternative parameterizations.

Doing so, users can be informed about the availability of alternative strategies to carry out the desired analysis, and select the most appropriate atom within the context of their experimental setup.

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Contributed atoms

DGE analysis (single-end reads)

Task	0		1			2		3
Operation	Data upload	Data organization (optional)	Quality control	Data preprocessing	Quality re-check (optional)	Genome alignment	Output sorting (optional)	Transcript quantification	Differential gene expression
Atoms	Galaxy data upload		FastQC	Cutadapt		BWA		AWK, Infer Experiment, featureCounts	DESeq2
				PRINSEQ		HISAT2
				Trimmomatic		Segemehl		AWK, Infer Experiment, HTSeq-ount
				Trim Galore!		STAR

Example: Galaxy data upload --> FastQC --> Cutadapt --> Segemehl --> AWK, Infer Experiment, featureCounts --> DESeq2

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DGE analysis (paired-end reads)

Task	0		1			2		3
Operation	Data upload	Data organization (optional)	Quality control	Data preprocessing	Quality re-check (optional)	Genome alignment	Output sorting (optional)	Transcript quantification	Differential gene expression
Atoms	Galaxy data upload	Galaxy create collections	FastQC	Cutadapt		BWA		AWK, Infer Experiment, featureCounts	DESeq2
				PRINSEQ		HISAT2
				Trimmomatic		STAR		AWK, Infer Experiment, HTSeq-ount
				Trim Galore!

Example: Galaxy data upload --> Galaxy create collections --> FastQC --> PRINSEQ --> STAR --> AWK, Infer Experiment, featureCounts --> DESeq2

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RRBS/BS-Seq analysis (paired-end reads)

Task	0		1			2		3		4
Operation	Data upload	Data organization (optional)	Quality control	Adapter clipping	Quality re-check (optional)	Quality trimming	Quality re-check (optional)	Genome alignment	Output sorting (optional)	Quantification of methylated reads
Atoms	Galaxy data upload	Galaxy create collections	FastQC	Cutadapt		PRINSEQ		Bismark		Samtools-filter, -sort, -fixmate, -markdup, -sort, MethylDackel, BEDtools-intersect intervals, -mergeBED, join, AWK
						Trimmomatic
						Trim Galore!

Example: Galaxy data upload --> Galaxy create collections --> FastQC --> Cutadapt --> Trimmomatic --> Bismark --> Samtools-filter, -sort, -fixmate, -markdup, -sort, MethylDackel, BEDtools-intersect intervals, -mergeBED, join, AWK

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How to contribute

Atoms can be tested, modified, and extended. The following sections will help you set up the Galaxy workflow generator to contribute with new atoms.

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Set up Docker

Set up Docker by following the same installation requirements needed to run the Galaxy workflow generator.

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When some tools are missing

New tools can be added in the Galaxy workflow generator by installing them...

1. From the admin panel (may load to unexpected errors upon execution)
2. Via re-building the docker image

Clone the Galaxy workflow generator:

$ git clone https://github.com/destairdenbi/galaxy-workflow-generator.git

Enter the cloned repository, and edit the tools.yaml file. New entries are described in the Markdown format.
The minimum set of metadata to be provided for each tool comprise:

• name
• owner
• tool_panel_section_label
• revisions

If unsure, please refer to the Galaxy Toolshed.

Once edited, you can build the Docker container locally:

$ docker build -t destair-local:latest .

Now run your local image and access it via a web browser:

$ docker run -d -p 8080:80 --name destair -v /absolute/path/to/local/directory/:/export destair-local:latest

for more parameters and further help, consult these instructions.

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When every tool is there

Atoms are interactive tours that illustrate one or more Galaxy tools.
For ease of use within the context of specific experimental setups, we suggest to build atoms that solve entire tasks of a target analysis, i.e. Adapter clipping, Quality control, Genome alignment, Transcript quantification, and so on.

You can create atoms by leveraging on the Galaxy Tour Builder. However, be aware that the Tour Builder cannot identify elements with a missing tour_id attribute, which means that the resulting tour's bubbles will not always be placed on the HTML elements of interest. This limitation is particularly visible on those elements that require an explicit user input, such as dropdowns, checkboxes, etc.
To overcome this problem, we defined some templates that can be used to place the interactive tour's bubble on the actual HTML elements of interest.
Check our TEMPLATES.md file for examples and use cases.

If your atom needs to be placed within an analysis which is not yet included in the Galaxy workflow generator, you need to create a new linker file. Look at the examples in the repository.
Otherwise, name the contributed atom with the label dgea_Xx.yaml, or bs_Xx.yaml. Where X is the task number, and x an identifier of your choice.

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Test new atoms

New atoms can be tested by running a Galaxy Docker container using a bind mount, or by running the Galaxy workflow generator using the interactive plugin.

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Option 1: Docker bind mount method

Run the Galaxy Docker container by creating a bind mount:

$ docker run -d -p 8080:80 --name destair -v /absolute/path/to/local/directory/:/export/ quay.io/destair/galaxy-workflow-generator:latest

for more parameters and further help, consult these instructions.

Once the container is ready, you will be able to copy the new atom into

/absolute/path/to/local/directory/export/galaxy-central/config/plugins/tours/

Now, either restart the running Galaxy instance and access it via a web browser locally localhost:8080:

$ docker exec destair supervisorctl restart galaxy:

or login to your Galaxy instance as administrator and run our de.STAIR plugin once with Update tours DB admin option checked.

New atoms will be automatically offered by our plugin and can be found by navigating the Galaxy interface under the header section Help -> Interactive Tours.

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Option 2: Local Galaxy setup method

• Set up the Galaxy environment
• Set up the de.STAIR atoms
• Contribute new atoms as stated above
• Set up the de.STAIR plugin
• Run the Galaxy framework

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