Your conda channels should be configured ideally in this order with strict channel priority order turned on:
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict
.condarc file should look something like:
channels: - conda-forge - bioconda - defaults channel_priority: strict
Conda can handle the creation of the environment for you directly:
conda create -n aviary -c bioconda aviary
Or install into existing environment:
conda install -c bioconda aviary
Create the environment using the
aviary.yml file then install from pip:
conda env create -n aviary -f aviary.yml conda activate aviary pip install aviary-genome
Initial requirements for aviary can be downloaded using the
git clone https://github.com/rhysnewell/aviary.git cd aviary conda env create -n aviary -f aviary.yml conda activate aviary pip install -e .
Whatever option you choose, running
aviary --help should return the following
......:::::: AVIARY ::::::...... A comprehensive metagenomics bioinformatics pipeline Metagenome assembly, binning, and annotation: assemble - Perform hybrid assembly using short and long reads, or assembly using only short reads recover - Recover MAGs from provided assembly using a variety of binning algorithms annotate - Annotate MAGs using EggNOG and GTBD-tk genotype - Perform strain diversity analysis of MAGs using Lorikeet complete - Runs each stage of the pipeline: assemble, recover, annotate, genotype in that order. cluster - Combines and dereplicates the MAGs from multiple Aviary runs using Galah Isolate assembly, binning, and annotation: isolate - Perform isolate assembly **PARTIALLY COMPLETED** Utility modules: configure - Set or overwrite the environment variables for future runs.
Upon first running aviary you will be prompted to input the location for where you would like your conda environments to be stored, the GTDB release installed on your system, the location of your EggNog database, and the location of your BUSCO database. These locations will be stored as environment variables, and automatically sourced by Aviary at runtime.
These environment variables can be reset using
Aviary uses programs which require access to locally stored databases. These databases can be quite large, as such we recommend setting up one instance of Aviary and these databases per machine or machine cluster.
The required databases are as follows:
Aviary can handle the download and installation of these databases via use of the
--download flag. Using
will download and install the databases into the folders corresponding to their associated environment variables. Aviary will
ask you to set these environment variables upon first running and if they are not already available. Otherwise, users can use
aviary configure subcommand to reset the environment variables:
aviary configure -o logs/ --eggnog-db-path /shared/db/eggnog/ --gtdb-path /shared/db/gtdb/ --checkm2-db-path /shared/db/checkm2db/ --download
This command will check if the databases exist at those given locations, if they don't then aviary will download and change the conda environment variables to match those paths.
N.B. Again, these databases are VERY large. Please talk to your sysadmin/bioinformatics specialist about setting a shared
location to install these databases to prevent unnecessary storage use. Additionally, the
--download flag can be used within
any aviary module to check that databases are configured properly.
Upon first running Aviary, you will be prompted to input the location for several database folders if
they haven't already been provided. If at any point the location of these folders change you can
use the the
aviary configure module to update the environment variables used by aviary.
These environment variables can also be configured manually, just set the following variables in your
export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release207/db/ # https://gtdb.ecogenomic.org/downloads export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.7/ # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.7#setup export CONDA_ENV_PATH=/path/to/conda/envs/
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