├── .circleci └── config.yml ├── .flake8 ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── LICENSE ├── README.md ├── docs ├── docs │ ├── CNAME │ ├── feature-reference │ │ ├── adding-and-updating-custom-databases.md │ │ ├── async-runs.md │ │ ├── authentication.md │ │ ├── output-objects.md │ │ ├── output-streaming.md │ │ └── using-aws-with-toolchest.md │ ├── getting-started │ │ ├── installation.md │ │ ├── python-functions-and-containers.md │ │ ├── running-bioinformatics-on-toolchest.md │ │ └── using-files.md │ ├── images │ │ └── toolchest_t.png │ ├── index.md │ ├── tool-reference │ │ ├── about.md │ │ ├── aligners.md │ │ ├── aligners │ │ │ ├── bowtie-2.md │ │ │ ├── clustal-omega.md │ │ │ ├── diamond.md │ │ │ ├── diamond │ │ │ │ ├── diamond-blastp.md │ │ │ │ └── diamond-blastx.md │ │ │ ├── kallisto.md │ │ │ ├── rapsearch2.md │ │ │ ├── salmon.md │ │ │ └── star.md │ │ ├── all-other-tools.md │ │ ├── assemblers.md │ │ ├── assemblers │ │ │ ├── megahit.md │ │ │ └── unicycler.md │ │ ├── demultiplexers.md │ │ ├── demultiplexers │ │ │ └── demucs.md │ │ ├── post-processing.md │ │ ├── post-processing │ │ │ └── bracken.md │ │ ├── pre-processing.md │ │ ├── pre-processing │ │ │ └── fastqc.md │ │ ├── python3.md │ │ ├── structure-prediction.md │ │ ├── structure-prediction │ │ │ └── alphafold.md │ │ ├── taxonomic-classifiers.md │ │ ├── taxonomic-classifiers │ │ │ ├── centrifuge.md │ │ │ ├── kraken-2.md │ │ │ └── metaphlan.md │ │ ├── test-runs.md │ │ ├── transfer.md │ │ ├── workflows-meta-tools.md │ │ └── workflows-meta-tools │ │ │ └── humann3.md │ └── toolchest-hosted-cloud │ │ ├── instance-types.md │ │ ├── pricing.md │ │ └── running-toolchest-in-your-aws-account.md └── mkdocs.yaml ├── poetry.lock ├── pyproject.toml ├── pytest.ini ├── tests ├── __init__.py ├── conftest.py ├── test_async.py ├── test_blastn.py ├── test_bowtie2.py ├── test_cellranger.py ├── test_centrifuge.py ├── test_chaining.py ├── test_clustalo.py ├── test_database_update.py ├── test_diamond.py ├── test_download.py ├── test_fastqc.py ├── test_filepath.py ├── test_humann3.py ├── test_kallisto.py ├── test_kraken2.py ├── test_last.py ├── test_megahit.py ├── test_metaphlan.py ├── test_output.py ├── test_public_uri.py ├── test_python3.py ├── test_rapsearch2.py ├── test_salmon.py ├── test_sanity.py ├── test_shi7.py ├── test_shogun.py ├── test_star.py ├── test_transfer.py ├── test_unicycler.py └── util │ ├── __init__.py │ ├── filter_output.py │ ├── hash.py │ ├── numpy_test.Dockerfile │ ├── s3.py │ └── streaming_script.py └── toolchest_client ├── __init__.py ├── api ├── __init__.py ├── auth.py ├── download.py ├── exceptions.py ├── instance_type.py ├── output.py ├── query.py ├── status.py ├── streaming.py └── urls.py ├── cli ├── __init__.py ├── cli.py ├── kraken2.py └── test.py ├── files ├── __init__.py ├── general.py ├── merge.py ├── public_uris.py ├── s3.py ├── split.py ├── tests │ ├── __init__.py │ ├── data │ │ ├── eight_line.fastq │ │ ├── eight_line_split_one.fastq │ │ ├── eight_line_split_two.fastq │ │ ├── paired_end │ │ │ ├── eight_line_R1.fastq │ │ │ └── eight_line_R2.fastq │ │ └── very_small_file.txt │ ├── test_general.py │ ├── test_merge.py │ ├── test_s3.py │ └── test_split.py └── unpack.py ├── logging.py └── tools ├── __init__.py ├── alphafold.py ├── api.py ├── blastn.py ├── bowtie2.py ├── bracken.py ├── cellranger.py ├── centrifuge.py ├── clustalo.py ├── demucs.py ├── diamond.py ├── fastqc.py ├── humann.py ├── jupyter.py ├── kallisto.py ├── kraken2.py ├── last.py ├── lug.py ├── megahit.py ├── metaphlan.py ├── python3.py ├── rapsearch2.py ├── salmon.py ├── shi7.py ├── shogun.py ├── star.py ├── test.py ├── tests ├── __init__.py ├── test_generic.py ├── test_kraken2.py ├── test_sanity.py └── test_star.py ├── tool.py ├── tool_args.py ├── transfer.py └── unicycler.py /.circleci/config.yml: -------------------------------------------------------------------------------- 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