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

Release Date Galaxy Tool Linting and Tests for push and PR

Description

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

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

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

Table of content

Installing FROGS-wrappers

Simplest way

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

It will install FROGS thanks to conda, download all these XML tools and well configure them in your Galaxy.

The 25 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 followingintegrated_tool_panel.xml file.

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

<section id="FROGS_3.2.3+galaxy2" name="FROGS" version="">

    <label id="FROGS_OTU_toolshed_3.2.3+galaxy2" text="OTUs reconstruction" version="" />

    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3+galaxy2" />    
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.3+galaxy2" />

    <label id="FROGSSTAT_Phyloseq_toolshed_3.2.3+galaxy2" text="OTUs structure and composition analysis" version="" />

    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3+galaxy2" />

    <label id="FROGSSTAT_DESeq_toolshed_3.2.3+galaxy2" text="Differential abundance analysis" version="" />

    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.3+galaxy2" />
    <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3+galaxy2" />
</section>

From sources

Prerequisites

You should start by installing 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 <Galaxy_Dir>/tools directory

(replace the) link to the new directory like this

ln -s <Galaxy_Dir>/tools/FROGS-wrappers-<Release_Number> <Galaxy_Dir>/tools/FROGS

  1. Add tools in galaxy

    Add the tools in <Galaxy_Dir>/config/tool_conf.xml

      <section id="frogs_local" name="FROGS local">
    <label id="frogs_otu_construction" text="OTUs reconstruction" />
    <tool file="FROGS/demultiplex.xml" />
    <tool file="FROGS/preprocess.xml" />
    <tool file="FROGS/clustering.xml" />
    <tool file="FROGS/remove_chimera.xml" />
    <tool file="FROGS/otu_filters.xml" />
    <tool file="FROGS/itsx.xml" />
    <tool file="FROGS/affiliation_OTU.xml" />
    <tool file="FROGS/affiliation_filters.xml" />
    <tool file="FROGS/affiliation_postprocess.xml" />
    <tool file="FROGS/normalisation.xml" />
    <tool file="FROGS/tree.xml" />
    <tool file="FROGS/clusters_stat.xml" />
    <tool file="FROGS/affiliations_stat.xml" />
    <tool file="FROGS/biom_to_stdBiom.xml" />
    <tool file="FROGS/biom_to_tsv.xml" />
    <tool file="FROGS/tsv_to_biom.xml" />
    <label id="frogsstat_phyloseq" text="OTUs structure and composition analysis" />
    <tool file="FROGS/phyloseq_import_data.xml" />
    <tool file="FROGS/phyloseq_composition.xml" />
    <tool file="FROGS/phyloseq_alpha_diversity.xml" />
    <tool file="FROGS/phyloseq_beta_diversity.xml" />
    <tool file="FROGS/phyloseq_clustering.xml" />
    <tool file="FROGS/phyloseq_structure.xml" />
    <tool file="FROGS/phyloseq_manova.xml" />
    <label id="frogsstat_deseq" text="Differential abundance analysis" />
    <tool file="FROGS/deseq2_preprocess.xml" />
    <tool file="FROGS/deseq2_visualisation.xml" />
  </section>

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

  2. 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:

    <section id="frogs_local" name="FROGS local" version="3_2_3">
        <label id="frogs_otu_construction" text="OTUs reconstruction" version="3_2_3" />
        <tool id="FROGS_demultiplex" />
        <tool id="FROGS_preprocess" />
        <tool id="FROGS_clustering" />
        <tool id="FROGS_remove_chimera" />
        <tool id="FROGS_OTU_filters" />
        <tool id="FROGS_itsx" />
        <tool id="FROGS_affiliation_OTU" />
        <tool id="FROGS_affiliation_filters" />
        <tool id="FROGS_affiliation_postprocess" />
        <tool id="FROGS_normalisation" />
        <tool id="FROGS_Tree" />
        <tool id="FROGS_clusters_stat" />
        <tool id="FROGS_affiliations_stat" />
        <tool id="FROGS_biom_to_stdBiom" />
        <tool id="FROGS_biom_to_tsv" />
        <tool id="FROGS_tsv_to_biom" />
        <label id="frogsstat_phyloseq" text="OTUs structure and composition analysis" version="3_2_3" />
        <tool id="FROGSSTAT_Phyloseq_Import_Data" />
        <tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" />
        <tool id="FROGSSTAT_Phyloseq_Alpha_Diversity" />
        <tool id="FROGSSTAT_Phyloseq_Beta_Diversity" />
        <tool id="FROGSSTAT_Phyloseq_Sample_Clustering" />
        <tool id="FROGSSTAT_Phyloseq_Structure_Visualisation" />
        <tool id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" />
        <label id="frogsstat_deseq" text="Differential abundance analysis" version="3_2_3" />
        <tool id="FROGSSTAT_DESeq2_Preprocess" />
        <tool id="FROGSSTAT_DESeq2_Visualisation" />
    </section>

  1. Add images

    Add the FROGS-wrappers images in <Galaxy_Dir>/static/images directory

    cp <Galaxy_Dir>/tools/FROGS/tools/frogs/static/images/* <Galaxy_Dir>/static/images/.

Use PEAR as reads merge software in preprocess

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 (<FROGS_DIR>/tools/preprocess/preprocess.xml):

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

    <conditional name="merge_software_type">
        <param name="merge_software" type="select" label="Merge software" help="Select the software to merge paired-end reads.">
            <option value="vsearch" selected="true">Vsearch</option>
            <option value="flash">Flash</option>
            <option value="pear">PEAR</option>
        </param>
        <when value="flash">
            <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" />
        </when>
    </conditional>

⚠️ 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.

  • 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://testtoolshed.g2.bx.psu.edu/view/oinizan/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.

  • Manual installation :

    • datatables : <Galaxy_Dir>/config/tool_data_table_conf.xml , example : <Galaxy_Dir>/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 : <Galaxy_Dir>/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 <FROGS_PATH>/app directory in the Galaxy PATH environment variable. (see environment-setup-file parameter ).

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 <Galaxy_dir>/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 <Galaxy_Dir>
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 <Galaxy_Dir>/config/galaxy.ini, create the corresponding <Galaxy_Dir>/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/FROGSSTAT_DESeq2_Preprocess/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3
toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3

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
    affiliation_OTU - 20 Gb 30 CPUs and 300 GB

  • Galaxy configuration

    You need to add destiantion sections (one per tool) in the <Galaxy-Dir>/config/job_conf.xml Example for SGE scheduler:

<destinations>
	...
	<destination id="FROGS_preprocess_job" runner="drmaa">
		<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
		<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
		<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
		<param id="nativeSpecification">-clear -q galaxyq -l mem=5G -l h_vmem=13G -pe parallel_smp 12</param>
	</destination>
	<destination id="FROGS_clustering_job" runner="drmaa">
		<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
		<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
		<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
		<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=10G -pe parallel_smp 16</param>
	</destination>
	<destination id="FROGS_remove_chimera_job" runner="drmaa">
		<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
		<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
		<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
		<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>
	</destination>
	<destination id="FROGS_itsx_job" runner="drmaa">
		<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
		<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
		<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
		<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>
	</destination>
	<destination id="FROGS_affiliation_OTU_job" runner="drmaa">
		<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
		<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
		<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
		<param id="nativeSpecification">-clear -q galaxyq -l mem=7G -l h_vmem=10G -pe parallel_smp 30</param>
	</destination>
</destinations>
<tools>
...
	<tool id="FROGS_preprocess" destination="FROGS_preprocess_job"/>   
	<tool id="FROGS_clustering" destination="FROGS_clustering_job"/>     
	<tool id="FROGS_remove_chimera" destination="FROGS_remove_chimera_job"/>
	<tool id="FROGS_itsx" destination="FROGS_itsx_job"/>
	<tool id="FROGS_affiliation_OTU" destination="FROGS_affiliation_OTU_job"/>
</tools>

License

GNU GPL v3

Copyright

2021 INRAE

Citation

Depending on which type of amplicon you are working on (mergeable or unmergeable), please cite one of the two FROGS publications:

Contact

[email protected]

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Galaxy wrappers for FROGS

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