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Galaxy workflow generator for assisted RNA-Seq and BS/RRBS-Seq analyses¶
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.
How it works¶
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.
Run the instance¶
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.
Installation requirements¶
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
Run the container¶
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.
Login credentials¶
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.
Update to a newer image¶
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:
Tools¶
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.
Quality control¶
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
Mapping¶
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
RNA-Seq¶
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
BS/RRBS-Seq¶
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
Utilities¶
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
Support¶
If you have questions, or don’t know how to solve a problem, please contact us here, or file an issue.
Contributing¶
New contributions are always welcome. Please read these instructions before proceeding in doing so.
MIT license¶
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.