galaxy-genome-annotation/docker-galaxy-genome-annotation

Name: docker-galaxy-genome-annotation

Owner: Galaxy Genome Annotation

Description: :whale: Galaxy Docker Image with Tools for Genome Annotation

Created: 2015-03-22 13:24:16.0

Updated: 2017-08-19 22:48:03.0

Pushed: 2017-12-18 11:01:55.0

Homepage:

Size: 88

Language: HTML

GitHub Committers

User	Most Recent Commit	# Commits
Anthony Bretaudeau	2018-02-22 14:43:34.0	22
Eric Rasche	2017-06-30 12:25:00.0	66
Björn Grüning	2017-06-30 09:40:00.0	12
Nathan Dunn	2017-06-29 12:12:36.0	4
Slugger70	2017-06-29 10:19:22.0	1

Other Committers

User	Email	Most Recent Commit	# Commits

README

Galaxy Image for Genome Annotation

er 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:

er 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:

er 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: admin@local.host) $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 admin@galaxy.org and the password admin. 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: https://github.com/peterjc/galaxy_blast/issues/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).

istory

2: Merge with the now-deprecated erasche version of this image.
1: Initial release!


upport & Bug Reports

support, questions, or feature requests, please [file bug reports on our github](https://github.com/galaxy-genome-annotation/docker-galaxy-genome-annotation/issues).


icence (MIT)

ission is hereby granted, free of charge, to any person obtaining a copy
his software and associated documentation files (the "Software"), to deal
he Software without restriction, including without limitation the rights
se, copy, modify, merge, publish, distribute, sublicense, and/or sell
es of the Software, and to permit persons to whom the Software is
ished to do so, subject to the following conditions:

above copyright notice and this permission notice shall be included in
copies or substantial portions of the Software.

SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
ESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
ORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
ILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
SOFTWARE.


upport

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