Galaxy Image for Genome Annotation

docker pull quay.io/galaxy-genome-annotation/docker-galaxy-annotation

For running the complete GMOD stack (including Apollo, Tripal, Chado), please see our other repository

A complete and production ready Galaxy instance for Genome Annotation.

• Installed tools
• Usage
• Users & Passwords
• Reproducibility of your search results
• Using large external BLAST databases
• Requirements
• Restarting Galaxy
• History
• Support & Bug Reports
• Licence (MIT)

Installed tools

• Assembly
  • Spades, Mira
• Structural Prediction
  • Glimmer
  • Augustus
• Functional Prediction
  • BLAST+
  • InterProScan
  • BLAST, Diamond, Blast2GO
• Utilities
  • FASTA manipulation tools
  • EMBOSS
• Comparative Genomics
  • CD-Hit, ClustalW
  • AntiSmash
  • mummer
• Annotation / Visualization
  • Apollo Tools
  • JBrowse-in-Galaxy
  • JBrowse-in-Galaxy Extras
  • Tripal Admin
  • Circos
• Automatic annotation
  • Prokka

Usage

You must have docker installed. Once that is available, it is as simple as:

docker run -d -p 8080:80 quay.io/galaxy-genome-annotation/docker-galaxy-annotation

If you only need the annotation / Visualization tools listed above, you can use a lighter Docker image:

docker run -d -p 8080:80 quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod

Please consult the docker manual for detailed explanations of available parameters. Please see bgruening/docker-galaxy-stable for more information on how to run this image.

Environment variables

The following environment variables must be set:

ENV	Use
$GALAXY_WEBAPOLLO_URL	The URL at which Apollo is accessible, internal to Galaxy and where the tools run. Must be absolute, with FQDN and protocol. (default: http://apollo:8080/apollo)
$GALAXY_WEBAPOLLO_USER	The admin user which Galaxy should use to talk to Apollo. (default: [email protected])
$GALAXY_WEBAPOLLO_PASSWORD	The password for the admin user. (default: password)
$GALAXY_WEBAPOLLO_EXT_URL	The external URL at which Apollo is accessible to end users. May be relative or absolute. (default: /apollo)
$GALAXY_SHARED_DIR	Directory shared between Galaxy and Apollo, used to exchange JBrowse instances. (default: /apollo-data)
$GALAXY_JBROWSE_SHARED_DIR	Directory shared between Galaxy and JBrowse, used to exchange JBrowse datasets. (default: /jbrowse/data)
$GALAXY_JBROWSE_SHARED_URL	The external URL at which JBrowse is accessible to end users. May be relative or absolute. (default: /jbrowse)
$GALAXY_TRIPAL_URL	The URL at which Tripal is accessible, internal to Galaxy and where the tools run. Must be absolute, with FQDN and protocol. (default: http://tripal/tripal/)
$GALAXY_TRIPAL_USER	The admin user which Galaxy should use to talk to Tripal. (default: admin)
$GALAXY_TRIPAL_PASSWORD	The password for the tripal admin user. (default: changeme)
$GALAXY_TRIPAL_SHARED_DIR	Directory shared between Galaxy and Tripal, used to exchange Tripal datasets. (default: /tripal-data)
$ASKOMICS_URL	The URL of a default AskOmics server. Users can override it in tool forms. (default: none)
$ENABLE_FIX_PERMS	Set this to 1 to let the container ensure that $GALAXY_SHARED_DIR, $GALAXY_JBROWSE_SHARED_DIR and $GALAXY_TRIPAL_SHARED_DIR are constantly world writable (chmod -R 777) (default: 1)

Users & Passwords

The Galaxy Admin User has the username [email protected] and the password password. If you want to create new users, please make sure to use the /export/ volume, otherwise all data will be removed whenever the container is restarted.

Reproducibility of Your Search Results

BLAST databases are updated daily and are not versioned. This is a general problem for reproducibility of search results. In Galaxy we track the program version, all settings and the input files. The underlying database can be tracked but this is usually very storage expensive. Note that the large NCBI BLAST databases exceeds 100 GB in size. To enable 100% reproducibility you can simply create your own BLAST datbase with Galaxy. Download your database as FASTA file and use the tool NCBI BLAST+ makeblastdb to convert your FASTA file to a proper BLAST database. These steps are reproducibly, with all settings and inputs.

If you want to use the precalculated BLAST databases from the NCBI FTP server you can configure your BLAST Galaxy instance to use those. Please have a look at Using large external BLAST databases. We have plans to make this a lot simples by using Galaxy data managers. You can track to progess here: peterjc/galaxy_blast#22

Please understand that we cannot ship the NCBI BLAST databases by default in this Docker container, as we try to keep the image as small as possible.

Using Large External BLAST Databases

You can get BLAST databases directly from the NCBI server and include them into your Galaxy docker container.

• Download your databases from ftp://ftp.ncbi.nlm.nih.gov/blast/db/. You can use the NCBI suggested perl script to automatize this step.
• Store all your BLAST databases in one directory, for example /galaxy_store/data/blast_databases/
• Start your Galaxy container with -v /galaxy_store/data/blast_databases/:/data/ to have access your databases inside of your container
• Start your Galaxy container with -v /home/user/galaxy_storage/:/export/ to export all config files to your host operating system
• Modify your blast*.loc files under /home/user/galaxy_storage/galaxy-central/tool-data/blast*.loc on your host, or under /export/galaxy-central/tool-data/blast*.loc from within your container.
• You need to add the paths to your blast databases. They need to look like /export/swissprot/swissprot
• Restart your Galaxy instance, for example with docker exec <container name> supervisorctl restart galaxy:

From now on you should see predifined BLAST databases in your Galaxy User Interface if you choose Locally installed BLAST database.

Restarting Galaxy

If you want to restart Galaxy without restarting the entire Galaxy container we can use docker exec (docker > 1.3).

docker exec <container name> supervisorctl restart galaxy:

History

• 0.2: Merge with the now-deprecated erasche version of this image.
• 0.1: Initial release!

Support & Bug Reports

For support, questions, or feature requests, please file bug reports on our github.

Licence (MIT)

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.

Support

This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)