Visit our web site : http://frogs.inrae.fr/
FROGS is a workflow designed to produce an ASV count matrix from high depth sequencing amplicon data.
FROGS also provide functionnal tools for functionnal abundance prediction, and statistical tools to explore ASV count table and taxonomical affiliations.
FROGS-wrappers allow to add FROGS on a Galaxy instance.
- Installing FROGS-wrappers
- Upload and configure the databanks
- Galaxy configuration
- License
- Copyright
- Citation
- Contact
FROGS and is data manager are available on the Toolshed (owner : frogs).
It will install FROGS thanks to conda, download XML tools and well configure them in your Galaxy.
The 28 FROGS tools are wrapped in 4 Galaxy tools:
- FROGS_Core tools is composed of a Main tools wrapper and a Companion tools wrapper, each including 8 FROGS tools : https://toolshed.g2.bx.psu.edu/view/frogs/frogs_core
- FROGS_Stat tool including 9 FROGS tools : https://toolshed.g2.bx.psu.edu/view/frogs/frogs_stat
- FROGS_Func tool including 3 FROGS tools: https://toolshed.g2.bx.psu.edu/view/frogs/frogs_func
To install FROGS-wrappers, you can follow the official Galaxy documentation : https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/. You may install tools via Galaxy admin interface or in commande line using Ephemeris.
For ephemeris, you can adapt the yaml file :
install_tool_dependencies: True
install_repository_dependencies: True
install_resolver_dependencies: True
tools:
- name: frogs_core
owner: frogs
tool_panel_section_label: FROGS
tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: frogs_stat
owner: frogs
tool_panel_section_label: FROGS
tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: frogs_func
owner: frogs
tool_panel_section_label: FROGS
tool_shed_url: https://toolshed.g2.bx.psu.edu/
This will create a FROGS section in your Galaxy tool panel, and install or update FROGS wrapper tools.
Databanks are defined in loc files and loc files are defined in Galaxy datatable.
In order to use the FROGS_Core tools, you must filled 3 datatables. We provide different databases for each of them that you simply need to download them and add them in the corresponding loc files.
-
Assignation databank (for taxonomic_affiliation wrapped tool)
URL : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
loc file :
frogs_db.loc
FROGS provides a data_manager (installable via the toolshed). It concerns only taxonomical assignation databank which are listed here : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv.
You may choose to download all formatted databases, or filter them on:
* date : all available database since DATE
* amplicon : ex: 16S
* base : ex: SILVA
* filters : this column is not always filled, but for example, we propose SILVA 16S database filtered on pintail score
* version : ex : 138.1
Datatables will be added in <Galaxy_Dir>/config/shed_tool_data_table_conf.xml
Loc files will be in : tool-data/toolshed.g2.bx.psu.edu/repos/frogs/frogs/<RANDOM>/
You may modify the directory where you want to store reference files by changing the galaxy_data_manager_data_path in the galaxy.yml files. All FROGS databases will be placed in a frogs_db directory.
Since FROGS-wrappers 3.2.3+galaxy2, FROGS datamanager have been published in it's own toolshed repository : https://toolshed.g2.bx.psu.edu/view/frogs/data_manager_frogs/
To remove previous installed datamanager, simply remove <data_manager> ... </data_manager> sections in your shed_data_manager_conf.xml galaxy config file.
Previously frogs_db.loc are in tool-data/toolshed.g2.bx.psu.edu/repos/frogs/frogs/*/frogs_db.loc and will still be available in all FROGS affiliation tools you have installed, do not remove it until you are sure that defined reference databases are useless.
-
Contaminant databank (cluster_filters wrapped tool)
URL : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants
loc file :
frogs_contaminant_db.loc -
Hyper variable in length amplicon databank (affiliation_postprocess wrapped tool)
URL : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL
loc file :
frogs_HVL.loc
In order to use the FROGS_Func tools, you must filled 3 other .loc files which must indicate the paths to the reference files of PICRUSt2 (present in the directory of the tool installed via conda) :
-
Reference tree file for placing ASV sequences (picrust2_placeseq_and_copynumber wrapped tool)
loc file :
frogs_picrust2_default_dir.loc -
Copy number of gene families present in referenced genomes (picrust2_functions wrapped tool)
loc file :
frogs_picrust2_marker_table.loc -
Pathways functionnal mapping file (picrust2_pathways wrapped tool)
loc file :
frogs_picrust2_pathway_map.loc
By default Galaxy sanitizes HTML outputs to prevent XSS attacks. FROGS, for almost all tools, outputs reports in HTML format. To allow their visualisation inside Galaxy, we need to avoid the Galaxy sanitization.
Via Galaxy admin interface and its Manage Allowlist menu, you can manage a whitelist of tools whose outputs will not be sanitized:
- FROGS Core 1-Main
- FROGS Core 2-Companion
- FROGS Func
- FROGS Stat
If you have more than one CPU, it is recommended to increase the number of CPUs used by tools.
All CPUs must be on the same computer/node.
-
Specifications
Tool CPU Total RAM FROGS Core 1-Main 16 48G or more FROGS Core 2-Companion - 10G or more FROGS Func 16 24G or more FROGS Stat - 10G or more -
Galaxy configuration
You need to add
destiantionsections (one per tool) in the<Galaxy-Dir>/config/job_conf.xml
GNU GPL v3
2025 INRAE
Depending on which type of amplicon you are working on (mergeable or unmergeable), please cite one of the two FROGS publications:
- Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.
- Bernard M., et al. Briefings in Bioinformatics, 2021. FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers.
frogs-support@inrae.fr