gpas-sc2 0.8.4

与全球病原体分析服务（https://www.gpas.cloud/）交互的命令行客户端。执行快速并行客户端去污和上传，并自动重命名下载的输出文件，以便使用原始样本标识符，同时保护隐私。支持使用Conda或Docker安装，并支持Ubuntu Linux、MacOS和Windows。

安装

使用conda

建议使用Miniconda（Miniconda安装指南）。如果使用的是最新的ARM架构Mac，您需要在Rosetta终端中安装Miniconda和gpas-cli（在Rosetta终端中安装Miniconda和gpas-cli）。

# Create and activate the conda environment
curl -OJ https://raw.githubusercontent.com/GlobalPathogenAnalysisService/gpas-cli/main/environment.yml
conda env create -f environment.yml
conda activate gpas-sc2

# Show gpas-cli version
gpas --version

# Updating? Run this before creating the conda environment
conda remove -n gpas-sc2 --all

使用docker

gpas-cli发行版已推送到Docker Hub，以便在大多数平台和架构上轻松安装。

# Fetch image, show gpas-cli version
docker run oxfordmmm/gpas-cli:latest gpas --version

# Fetch image, upload example data using a bound volume
docker run \
-v /Users/bede/Research/Git/gpas-cli/tests/test-data:/test-data \
oxfordmmm/gpas-cli:latest \
gpas upload \
--environment dev \
--token /test-data/token.json \
--out-dir /test-data/output \
/test-data/large-nanopore-bam.csv

# Build image from scratch, show gpas-cli version
curl -OJ https://raw.githubusercontent.com/GlobalPathogenAnalysisService/gpas-cli/main/Dockerfile
docker run --rm $(docker build -q .) gpas --version

# Build image from scratch, upload example data
docker run \
-v /Users/bede/Research/Git/gpas-cli/tests/test-data:/test-data \
$(docker build -q .) \
gpas upload \
--environment dev \
--token /test-data/token.json \
--out-dir /test-data/output \
/test-data/large-nanopore-bam.csv

使用pip

可以在Python 3.10+环境中使用pip install安装PyPI软件包，并手动安装samtools和readItAndKeep的二进制依赖项。

# Install inside a new Python environment
python3 -m venv gpas-sc2
source gpas-sc2/bin/activate
pip install gpas

# Show gpas-cli version
gpas --version

# If samtools and read-it-and-keep are not in $PATH, tell gpas-cli where to find them
export GPAS_SAMTOOLS_PATH=path/to/samtools
export GPAS_READITANDKEEP_PATH=path/to/readItAndKeep

使用PyInstaller

为每个发行版生成静态Linux、MacOS和Windows可执行文件。这些可执行文件旨在与GUI客户端一起分发，但也可以独立使用。这些可以从以下每个工作流程运行的“工件”部分下载：[链接](https://github.com/GlobalPathogenAnalysisService/gpas-cli/actions/workflows/distribute.yml)

身份验证

大多数gpas-cli操作都需要有效的API令牌（token.json）。这可以通过在GPAS门户的“上传客户端”页面上的“获取API令牌”按钮保存。如果您看不到此按钮，请要求GPAS团队为您启用它。如果您想尝试GPAS，请与我们联系！

命令行用法

gpas validate

验证upload_csv并检查其引用的fastq或bam文件是否存在。

gpas validate large-nanopore-fastq.csv

# Validate supplied tags
gpas validate --environment dev --token token.json large-nanopore-fastq.csv

% gpas validate -h
usage: gpas validate [-h] [--token TOKEN] [--environment {dev,staging,prod}] [--json-messages] upload_csv

Validate an upload CSV. Validates tags remotely if supplied with an authentication token

positional arguments:
  upload_csv            Path of upload CSV

options:
  -h, --help            show this help message and exit
  --token TOKEN         Path of auth token available from GPAS Portal
                        (default: None)
  --environment {dev,staging,prod}
                        GPAS environment to use
                        (default: prod)
  --json-messages       Emit JSON to stdout
                        (default: False)

gpas upload

验证、去污并将upload_csv中指定的读取上传到指定的GPAS环境。

gpas upload --environment dev --token token.json large-illumina-bam.csv

# Dry run; skip submission
gpas upload --dry-run --environment dev --token token.json large-illumina-bam.csv

# Offline mode; quit after decontamination
gpas upload tests/test-data/large-nanopore-fastq.csv

% gpas upload -h
usage: gpas upload [-h] [--token TOKEN] [--working-dir WORKING_DIR] [--out-dir OUT_DIR] [--processes PROCESSES] [--dry-run]
                   [--debug] [--environment {dev,staging,prod}] [--json-messages]
                   upload_csv

Validate, decontaminate and upload reads to the GPAS platform

positional arguments:
  upload_csv            Path of upload csv

options:
  -h, --help            show this help message and exit
  --token TOKEN         Path of auth token available from GPAS Portal
                        (default: None)
  --working-dir WORKING_DIR
                        Path of directory in which to make intermediate files
                        (default: /tmp)
  --out-dir OUT_DIR     Path of directory in which to save mapping CSV
                        (default: .)
  --processes PROCESSES
                        Number of tasks to execute in parallel. 0 = auto
                        (default: 0)
  --dry-run             Exit before submitting files
                        (default: False)
  --debug               Emit verbose debug messages
                        (default: False)
  --environment {dev,staging,prod}
                        GPAS environment to use
                        (default: prod)
  --json-messages       Emit JSON to stdout
                        (default: False)

gpas download

通过传递在批量上传期间生成的mapping_csv或逗号分隔的样本guid列表，从GPAS平台下载json、fasta、vcf和bam输出。通过传递--mapping-csv和--rename，使用本地样本名称保存输出文件，而不需要平台的了解。

# Download and rename BAMs for a previous upload
gpas download --rename --mapping-csv C-a06cbab8.mapping.csv --file-types bam token.json

# Download all outputs for a single guid
gpas download --guids 6e024eb1-432c-4b1b-8f57-3911fe87555f --file-types json,vcf,bam,fasta token.json

% gpas download -h
usage: gpas download [-h] [--mapping-csv MAPPING_CSV] [--guids GUIDS] [--file-types FILE_TYPES] [--out-dir OUT_DIR] [--rename]
                     [--debug] [--environment {dev,staging,prod}]
                     token

Download analytical outputs from the GPAS platform for given a mapping csv or list of guids

positional arguments:
  token                 Path of auth token (available from GPAS Portal)

options:
  -h, --help            show this help message and exit
  --mapping-csv MAPPING_CSV
                        Path of mapping CSV generated at upload time
                        (default: None)
  --guids GUIDS         Comma-separated list of GPAS sample guids
                        (default: )
  --file-types FILE_TYPES
                        Comma separated list of outputs to download (json,fasta,bam,vcf)
                        (default: fasta)
  --out-dir OUT_DIR     Path of output directory
                        (default: /Users/bede/Research/Git/gpas-cli)
  --rename              Rename outputs using local sample names (requires --mapping-csv)
                        (default: False)
  --debug               Emit verbose debug messages
                        (default: False)
  --environment {dev,staging,prod}
                        GPAS environment to use
                        (default: prod)

gpas status

通过传递在上传时生成的mapping_csv或逗号分隔的样本guid列表，检查已上传批次的处理状态。

gpas status --mapping-csv example_mapping.csv --environment dev token.json
gpas status --guids 6e024eb1-432c-4b1b-8f57-3911fe87555f --format json token.json

% gpas status -h
usage: gpas status [-h] [--mapping-csv MAPPING_CSV] [--guids GUIDS] [--format {table,csv,json}] [--rename] [--raw]
                   [--environment {dev,staging,prod}]
                   token

Check the status of samples submitted to the GPAS platform

positional arguments:
  token                 Path of auth token available from GPAS Portal

options:
  -h, --help            show this help message and exit
  --mapping-csv MAPPING_CSV
                        Path of mapping CSV generated at upload time
                        (default: None)
  --guids GUIDS         Comma-separated list of GPAS sample guids
                        (default: )
  --format {table,csv,json}
                        Output format
                        (default: table)
  --rename              Use local sample names (requires --mapping-csv)
                        (default: False)
  --raw                 Emit raw response
                        (default: False)
  --environment {dev,staging,prod}
                        GPAS environment to use
                        (default: prod)

开发和测试

使用pre-commit在提交时应用black风格（应自动发生）

git clone https://github.com/GlobalPathogenAnalysisService/gpas-cli
cd gpas-cli
conda env create -f environment-dev.yml
conda activate gpas-sc2-dev
pip install --upgrade --force-reinstall --editable ./

# Offline unit tests
pytest tests/test_gpas.py

# The full test suite requires a valid token for dev inside tests/test-data
pytest --cov=gpas