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https://github.com/bebatut/frogs-wrappers

Galaxy wrappers for FROGS

https://github.com/bebatut/frogs-wrappers

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Repository

Galaxy wrappers for FROGS

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  • Host: GitHub
  • Owner: bebatut
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Fork of geraldinepascal/FROGS-wrappers
Created about 2 years ago · Last pushed about 2 years ago

https://github.com/bebatut/FROGS-wrappers/blob/master/ 


 
  
 



Visit our web site : http://frogs.toulouse.inrae.fr/

[![Release](https://img.shields.io/badge/release-4.1.0+galaxy1-blue.svg)](https://github.com/geraldinepascal/FROGS-wrappers/releases)   ![Date](https://img.shields.io/badge/date-May%202023-red.svg)   [![Galaxy Tool Linting and Tests for push and PR](https://github.com/geraldinepascal/FROGS-wrappers/actions/workflows/pr.yaml/badge.svg?branch=master)](https://github.com/geraldinepascal/FROGS-wrappers/actions/workflows/pr.yaml)   [](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web)




# Description

FROGS is a workflow designed to produce an ASV count matrix from high depth sequencing amplicon data.

FROGS also provide statistical tools to explore ASV count table and taxonomical affiliations.

FROGS-wrappers allow to add FROGS on a Galaxy instance.

# Table of content

* [Installing FROGS\-wrappers](#installing-frogs-wrappers)
  * [Simplest way](#simplest-way)
  * [From sources](#from-sources)
      * [Prerequisites](#prerequisites)
      * [FROGS\-wrappers installation](#frogs-wrappers-installation)
* [Use PEAR as reads merge software in preprocess](#use-pear-as-reads-merge-software-in-preprocess)
* [Upload and configure the databanks](#upload-and-configure-the-databanks)
* [Galaxy configuration](#galaxy-configuration)
  * [Setup Galaxy environment variables](#setup-galaxy-environment-variables)
  * [Install python packages inside virtual env](#install-python-packages-inside-virtual-env)
  * [Avoid FROGS HTML report sanitization](#avoid-FROGS-HTML-report-sanitization)
  * [Set memory and parallelisation settings](#set-memory-and-parallelisation-settings)
* [License](#license)
* [Copyright](#copyright)
* [Citation](#citation)
* [Contact](#contact)

# Installing FROGS-wrappers

## Simplest way

FROGS and is data manager are available on the Toolshed (owner : frogs).

It will install FROGS thanks to [conda](https://anaconda.org/bioconda/frogs), download all these XML tools and well configure them in your Galaxy.

The 28 FROGS tools will be in random order in your tools panel. We propose to control that order by modifying the `shed_tool_conf.xml`  which will render the following`integrated_tool_panel.xml ` file.

We suppose that you installed FROGS in a specific section named `FROGS`.

```



    

```



## From sources

#### Prerequisites

You should start by installing [FROGS](https://github.com/geraldinepascal/FROGS) (remember, FROGS is now installable via conda ).

#### FROGS-wrappers installation

1.    Download wrapper

   Download the last released versions of FROGS-wrappers: https://github.com/geraldinepascal/FROGS-wrappers/releases

   Uncompress and unarchive the release in your ` /tools` directory

   (replace the) link to the new directory like this

   ` ln -s /tools/FROGS-wrappers-  /tools/FROGS`

2. Add tools in galaxy

   Add the tools in `/config/tool_conf.xml`

   ```
     

       
     
   ```
   NB: If you used previous version of FROGS (<3.1), you must removed `app` direcotry name in the paths names.

3.  Correct tools order

Tools order in the Galaxy interface will not follow the tool_conf.xml definition.

Modify manually the `galaxy_dir/config/integrated_tool_panel.xml`:

```
    

        

```


1. Add images

   Add the FROGS-wrappers images in `/static/images` directory

   `cp /tools/FROGS/tools/frogs/static/images/* /static/images/.`


# Use PEAR as reads merge software in preprocess
[PEAR](https://cme.h-its.org/exelixis/web/software/pear/) is one of the most effective software for read pair merging, but as its licence is not free for private use, we can not distribute it in FROGS.
If you work in an academic lab on a private Galaxy server, or if you have payed your licence you can use PEAR in FROGS preprocess.
For that, you need to:

* have PEAR in your PATH or in the FROGS libexec directory

* add PEAR in the FROGS-wrappers preprocess Galaxy wrapper (`/tools/preprocess/preprocess.xml`):

  :warning: there is two places where the list `merge_software` is defined, add pear in both of them!

```
    
        
            
            
            
        
        
            
        
    
```

:warning: remember, there is two places where the list `merge_software` is defined, add pear in both of them!

# Upload and configure the databanks

Databanks are defined in `loc` files and `loc` files are defined in Galaxy datatable.

We provide some databanks for each of these 3 data tables, you simply need to download them and add them in the corresponding `loc` files.


- Assignation databank for taxonomic_affiliation 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 `/config/shed_tool_data_table_conf.xml` 

Loc files will be in : `tool-data/toolshed.g2.bx.psu.edu/repos/frogs/frogs//`

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 ` ... ` 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 for cluster_filter tool

  URL : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants

  loc file : `frogs_contaminant_db.loc`
  

- Hyper variable in length amplicon databank for affiliation_postprocess tool

  URL : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL

  loc file : `frogs_HVL.loc`
  

In order to use the FROGSFUNC tools, you must also create 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 for example) :

- Place studied sequences ((.e. ASVs) into a reference tree, for frogsfunc_step1 tool
  
  loc file : `frogs_picrust2_default_dir.loc`
  

- Predict the copy number of gene families present in the predicted genome for ASV, for frogsfunc_step2 tool
  
  loc file : `frogs_picrust2_marker_table.loc`
  

- Map pathways to reactions, , for frogsfunc_step3 tool
  
  loc file : `frogs_picrust2_pathway_map.loc`


**Manual installation** :

  * datatables : `/config/tool_data_table_conf.xml` , example : `/tools/FROGS/tools/frogs/tool_data_table_conf.xml.sample`

    Add FROGS-wrappers datatables in the Galaxy datatables, but replace `{__HERE__}` by `tools/FROGS/tools/frogs `.

  * loc files example : `/tools/FROGS/tools/frogs/tool-data/`

    Copy and rename them as indicated in the tool_data_table.

    Then add entry as indicated in each loc files.

# Galaxy configuration

## setup Galaxy environment variables

FROGS python programs (and all dependencies) need to be available in the PATH, if not installing from the toolshed, you need to add `/app` directory in the Galaxy PATH environment variable. (see [environment-setup-file parameter](https://docs.galaxyproject.org/en/latest/admin/config.html#environment-setup-file) ).

You can also activate `conda` as tool dependency resolver (https://docs.galaxyproject.org/en/latest/admin/conda_faq.html) by setting `conda_prefix` path and `conda_auto_install ` to `true` in the `/config/galaxy.yml` configuration file.

## Install python packages inside virtual env

Galaxy runs in a specific virtual env. To allow FROGS clusters stat to access to the python scipy library, you may need to (re)install it inside the Galaxy virtual env
```
cd 
source .venv/bin/activate
pip install scipy
deactivate
```

## Avoid FROGS HTML report sanitization

By default Galaxy sanitizes HTML outputs to prevent XSS attacks.
FROGS outputs, for almost all tools, report in HTML format. To allow their visualisation inside Galaxy, we need to avoid the Galaxy sanitization.
You need to uncomment `sanitize_whitelist_file` line in `/config/galaxy.ini`, create the corresponding `/config/sanitize_whitelist.txt` file if not already done, and add the following lines in it. You may also manage it from the Admin interface of Galaxy in the `Manage Allowlist` section.

```
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSFUNC_step1_placeseqs/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSFUNC_step2_functions/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSFUNC_step3_pathways/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_stats/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_cluster_filters/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_cluster_stats/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_taxonomic_affiliation/4.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/4.1.0+galaxy1

```

## Set memory and parallelisation settings

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          | RAM per CPU | Minimal RAM | Configuration example |
     | :-------------------: | :---------: | :---------: | :-------------------: |
     |      preprocess       |     8Gb     |      -      |   12 CPUs and 96 GB   |
     |      clustering       |      -      |    10 Gb    |   16 CPUs and 60 GB   |
     | ITSx / remove_chimera |     3Gb     |     5Gb     |   12 CPUs and 36 GB   |
     |    taxonomic_affiliation    |      -      |    20 Gb    |  30 CPUs and 300 GB   |

   * Galaxy configuration

     You need to add `destiantion` sections (one per tool) in the `/config/job_conf.xml`
     Example for SGE scheduler:


```

	...
	
		scripts/drmaa_external_runner.py
		scripts/drmaa_external_killer.py
		scripts/external_chown_script.py
		-clear -q galaxyq -l mem=5G -l h_vmem=13G -pe parallel_smp 12
	
	
		scripts/drmaa_external_runner.py
		scripts/drmaa_external_killer.py
		scripts/external_chown_script.py
		-clear -q galaxyq -l mem=3G -l h_vmem=10G -pe parallel_smp 16
	
	
		scripts/drmaa_external_runner.py
		scripts/drmaa_external_killer.py
		scripts/external_chown_script.py
		-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12
	
	
		scripts/drmaa_external_runner.py
		scripts/drmaa_external_killer.py
		scripts/external_chown_script.py
		-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12
	
	
		scripts/drmaa_external_runner.py
		scripts/drmaa_external_killer.py
		scripts/external_chown_script.py
		-clear -q galaxyq -l mem=7G -l h_vmem=10G -pe parallel_smp 30
	


...
	   
	     
	
	
	

```

# License
    GNU GPL v3

# Copyright
    2022 INRAE

# Citation

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.*](https://doi.org/10.1093/bioinformatics/btx791)
* [*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.*](https://doi.org/10.1093/bib/bbab318)

# Contact
    frogs-support@inrae.fr

Owner

  • Name: Bérénice Batut
  • Login: bebatut
  • Kind: user
  • Location: Clermont-Ferrand, France
  • Company: University of Freiburg

@galaxyproject training, @usegalaxy-eu, @open-life-science, @StreetScienceCommunity, @gallantries

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