With contributions from a growing community of developers and users, the number
of alternative Galaxy tools addressing the same questions has steadily risen.
For this reason, it has become harder for the user to make informed decisions
on the selection of tools, and their parameterization.
The Galaxy training material
has helped sharing best-practices where novice and expert users can learn new
methods to carry out their analyses. However, tools are pre-selected by the
community, and the absence of a systematic overview of the available
alternative tools of a Galaxy instance, does not train users on how to evaluate
alternative algorithms and parameterizations.
The Galaxy workflow generator provides an overview of the available alternative tools that users can use to build RNA-Seq and BS-Seq analyses. Here, users are presented with new interactive pop-ups to compare and evaluate the suitability of each tool during the course of the analysis.
The Galaxy workflow generator presents a different way of how to assist in
the creation of Galaxy workflows. Here, single or multiple alternative Galaxy
tools are provided as an atom: an interactive tour that illustrates tool
options and parameterizations within the context of a selected analysis.
In this Galaxy instance, we provide sample analyses organized into their
logical tasks. For example, an RNA-Seq analysis is organized into:
- Task 1: Quality control and data preprocessing
- Task 2: Genome alignment
- Task 3: Transcript quantification and differential gene expression
Each task can be completed by means of one or more alternative atoms.
The Galaxy workflow generator embeds a plugin that extends the Galaxy
interface with novel interactive dialogs, which compare the alternative atoms
that can be used to solve the current task in the selected analysis. Doing so,
we are able to inform users about alternative tools and parameterizations.
The Figure below illustrates how the process of selecting atoms and building workflows takes place. Here, a user is carrying out an RNA-Seq analysis, which is divided into its three tasks: 1) Quality control and data preprocessing, 2) Genome alignment, 3) Transcript quantification and differential gene expression. For each task, the user selects the desired atom in the front-end interface, and navigates the corresponding interactive tour. The interactive tour drives the execution of each underlying tool in the Galaxy back-end. Once each task has been completed, the resulting workflow (traced in red), will thus be composed of the series of alternative tools of each selected atom, parameterized according to the interactive tour.
The Galaxy workflow generator collects alternative atoms to carry out RNA-Seq and BS/RRBS-Seq analyses.
The Galaxy workflow generator can run on you machine. The following sections will help you set up and run the instance. Optional, have a look here for more detailed information.
The only requirement is Docker, which can be installed in different ways depending on the underlying system:
- Unix users should follow the Docker installation for Linux
- MacOS 10.12+ users should follow the Docker installation for Mac
- Windows 10+ users, should follow the Docker installation for Windows
- Non-unix users, whose operative system version is older than the aforementioned one, can rely on Kitematic
Users not relying on Kitematic can open a terminal, or a Windows PowerShell, and type:
$ docker run --net bridge -d -p 8080:80 --name destair quay.io/destair/galaxy-workflow-generator:latest
To allow the use of multiple threads, please prefix the aforementioned command in the following way:
$ docker run -e "GALAXY_CONFIG_PARALLEL_SLURM_PARAMS=--ntasks=8" \ -e "GALAXY_CONFIG_PARALLEL_LOCAL_NTASKS=8" ...To store users and data permanently, mount a directory on your harddrive into the containers /export directory by adding the following parameter:
$ -v /absolute/path/to/local/directory:/exportTo use an other user account rather than the default admins, to allow for anonoymous workflow generation prefix the command the following way and create the new user afterwards:
$ docker run -e "GALAXY_DEFAULT_WORKFLOWGENERATOR_USER=username@to-be.created"
Kitematic users can launch the Galaxy instance by following these instructions.
After running the container, the Galaxy instance can be accessed from the local
web browser, at the address localhost:8080.
We recommend using Google Chrome, Chromium, or Mozilla Firefox.
To be able to analyse data, users need to be logged in.
- Galaxy users can create an account by clicking on the
Login or Registerbutton, on the top header - Galaxy administrators can use the default credentials username:
admin, password:admin, and then change settings later on.
Stop the running container.
$ docker stop destair
Pull the latest image
$ docker pull quay.io/destair/galaxy-workflow-generator:latest
Run the new image as described above
In case a bind mount (-v parameter, see above) was used, upgrades on atoms and tours can be found, compared and copied from the following locations.
$ cp -r /absolute/path/to/local/directory/.distribution_config/plugins/webhooks/* /absolute/path/to/local/directory/galaxy-central/plugins/webhooks
$ cp /absolute/path/to/local/directory/.distribution_config/plugins/tours/*.yaml /absolute/path/to/local/directory/galaxy-central/plugins/tours/
Now restart Galaxy
$ docker exec destair supervisorctl restart galaxy:
The tools catalog is bound to be modified and expanded during the development
of the Galaxy workflow generator.
The following list provides an overview of the tools that have been installed so far.
| Tool | Description | Reference |
|---|---|---|
| Cutadapt | Error-tolerant adapter removal tool for High-Throughput Sequencing reads | Martin 2011 |
| FastQC | A quality control tool for high throughput sequence data | Andrews |
| PRINSEQ | A quality control and data preprocessing tool for metagenomic data | Schmieder and Edwards 2011 |
| Trim Galore! | Quality control tool for read trimming and filtering of NGS data | |
| Trimmomatic | Quality control tool for read trimming and filtering of Illumina NGS data | Bolger et al. 2014 |
| Tool | Description | Reference |
|---|---|---|
| BWA | Burrows-Wheeler Aligner for mapping low-divergent sequences against a large reference genome | Li and Durbin 2010 |
| bwameth | Fast and accurate aligner of BS-Seq reads | Brent et al. 2014 |
| HISAT2 | Hierarchical indexing for spliced alignment of transcripts | Pertea et al. 2016 |
| segemehl | Short sequence read to reference genome mapper | Otto et al. 2014 |
| STAR | Rapid spliced aligner for RNA-seq data | Dobin et al. 2013 |
| Tool | Description | Reference |
|---|---|---|
| BWA | Burrows-Wheeler Aligner for mapping low-divergent sequences against a large reference genome | Li and Durbin 2010 |
| DESeq2 | Differential gene expression analysis based on the negative binomial distribution | Love et al. 2014 |
| featureCounts | Genomic feature read count tool for summarising of genes, exons, and promoter counts | Liao et al. 2014 |
| HISAT2 | Hierarchical indexing for spliced alignment of transcripts | Pertea et al. 2016 |
| HTSeq-count | Tool for counting reads in features | Anders et al. 2015 |
| Rcorrector | A kmer-based error correction method for RNA-seq data | Song et al. 2015 |
| RSeQC | An RNA-seq Quality Control Package | Wang et al. 2012 |
| SortMeRNA | A tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and -genomic data | Kopylova et al. 2011 |
| STAR | Rapid spliced aligner for RNA-seq data | Dobin et al. 2013 |
| Tool | Description | Reference |
|---|---|---|
| Bismark | A program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls | Krueger et al. 2011 |
| bwameth | Fast and accurate aligner of BS-Seq reads | Brent et al. 2014 |
| MethylDackel | A tool to extract per-base methylation metrics from coordinate-sorted and indexed BS-seq alignments | Ryan |
| segemehl | Short sequence read to reference genome mapper | Otto et al. 2014 |
| Tool | Description | Reference |
|---|---|---|
| SAMtools | Utilities for manipulating alignments in the SAM format | Heng et al. 2009 |
| BEDTools | Utilities for genome arithmetic | Quinlan et al. 2010 |
The Galaxy workflow generator incorporates a set of sample workflows that are
created using the de.STAIR Galaxy atoms.
Workflows cover Differential gene expression analyses (single-end and
paired-end reads) and RRBS/BS-Seq analyses (paired-end reads), and are
collected in their dedicated repository.
If you have questions, or don't know how to solve a problem, please contact us here, or file an issue.
New contributions are always welcome. Please read these instructions before proceeding in doing so.
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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