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توضیحات

aviary - metagenomics pipeline using long and short reads

ویژگی	مقدار
سیستم عامل	-
نام فایل	aviary-genome-0.5.7
نام	aviary-genome
نسخه کتابخانه	0.5.7
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Rhys Newell
ایمیل نویسنده	rhys.newell94@gmail.com
آدرس صفحه اصلی	https://github.com/rhysnewell/aviary
آدرس اینترنتی	https://pypi.org/project/aviary-genome/
مجوز	GPL-3.0

![](docs/_include/images/aviary_logo.png) # Aviary An easy to use for wrapper for a robust snakemake pipeline for metagenomic short-read, long-read, and hybrid assembly. Aviary also performs binning, annotation, strain diversity analyses,a nd provides users with an easy way to combine and dereplicate many aviary results with rapidity. The pipeline currently includes a series of distinct, yet flexible, modules that can seamlessly communicate with each other. Each module can be run independently or as a single pipeline depending on provided input. [Please refer to the full docs here](https://rhysnewell.github.io/aviary) # Quick Installation 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 ``` Your resulting `.condarc` file should look something like: ``` channels: - conda-forge - bioconda - defaults channel_priority: strict ``` #### Option 1) Install from Bioconda 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 ``` #### Option 2) Install from pip 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 ``` #### Option 3) Install from source Initial requirements for aviary can be downloaded using the `aviary.yml`: ``` 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 output: ``` ......:::::: 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 EnrichM database, and the location of your BUSCO database. These locations will be stored as environment variables, but for aviary to be able to use those environment variables you will have to either source your .bashrc or reactivate your conda environment depending on whether you installed aviary within a conda environment or not: ``` conda deactivate; conda activate aviary OR source ~/.bashrc ``` These environment variables can be reset using `aviary configure` ## Databases 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: * [GTDB](https://gtdb.ecogenomic.org/downloads) * [EggNog](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup) * [CheckM2](https://github.com/chklovski/CheckM2) ### Installing databases Aviary can handle the download and installation of these databases via use of the `--download` flag. Using `--download` 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 the `aviary configure` subcommand to reset the environment variables: ```commandline 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. ### Environment variables 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 `.bashrc` file: ``` export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release207/db/ # https://gtdb.ecogenomic.org/downloads export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.8/ # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup export CHECKM2DB=/path/to/checkm2db/ export CONDA_ENV_PATH=/path/to/conda/envs/ ``` # Workflow ![Aviary workflow](figures/aviary_workflow.png) # Citations If you use aviary then please be aware that you are using a great number of other programs and aviary wrapping around them. You should cite all of these tools as well, or whichever tools you know that you are using. To make this easy for you we have provided the following list of citations for you to use in alphabetical order. This list will be updated as new modules are added to aviary. A constantly updating list of citations can be found in the [Citations document](https://rhysnewell.github.io/aviary/citations). # License Code is [GPL-3.0](LICENSE)

نحوه نصب

نصب پکیج whl aviary-genome-0.5.7:

pip install aviary-genome-0.5.7.whl

نصب پکیج tar.gz aviary-genome-0.5.7:

pip install aviary-genome-0.5.7.tar.gz