Galaxy Image for Genomic Variant Analysis

🐳 Galaxy Docker repository for genomic variant analysis from NGS data (Galaxy Variant Analysis flavor)

Installed tools

• BWA
• Bowtie2
• SnpEff
• FASTQC
• SAMTools
• FreeBayes
• VarScan
• lofreq
• GEMINI
• deepTools
• MultiQC
• Qualimap
• JBrowse
• Circos

Requirements

• Docker for Linux / Windows / OSX
• podman as a convenient alternative for rpm-based Linux distributions
• Kitematic for Windows / OS-X

Training

To learn what kind of analyses you can perform with this Galaxy flavor, have a look at the following Galaxy training network tutorials:

• Exome sequencing data analysis for diagnosing a genetic disease
• Identification of somatic and germline variants from tumor and normal sample pairs
• Mapping and molecular identification of phenotype-causing mutations

Usage

To launch:

docker run -d -p 8080:80 -p 8021:21 -p 8022:22 bgruening/galaxy-exome-seq

For more details about this command line or specific usage, please consult the README of the main Galaxy Docker image, on which the current image is based.

Advanced cluster configuration

Galaxy and every tool can be configured to make optimal usage of cluster resources. For this a configuration file with the name job_conf.xml is needed. You can read more about this with more details in the upstream documentation or by studying advanced examples configurations.

For the Miracum project we have included one example job_conf.xml. This example configuration uses SLURM as scheduler and assignes 8 cores (slurm-8c) to the tools lofreq_call and bwa_mem. By default every tool gets one core.

To use this example configuration, or another one, please copy the job_conf.xml.miracum_sample in your export folder into the Galaxy config folder (e.g. export/galaxy-central/config/job_conf.xml). If you copy your file to a different place (it needs to be accessible from inside the container) you can also point Galaxy duing startup to this special config file with: -e GALAXY_CONFIG_JOB_CONFIG_FILE=/export/job_conf.xml

Update Chrom-size files

From time to time, especially if you want to add new reference genome, it might be necessary to also deploy new chrom-size files. You can do this with

docker exec -t -i your_galaxy_conainer bash
cd /galaxy-central
python ./cron/build_chrom_db.py /export/galaxy-central/tool-data/shared/ucsc/chrom/

Contributors

• Bjoern Gruening
• Bérénice Batut
• Wolfgang Maier

Support & Bug Reports

You can file a github issue or ask us on the Galaxy help forum.