blast2galaxy：用于在Galaxy服务器上进行BLAST+和DIAMOND搜索的命令行界面和Python应用程序编程接口。
blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers.
作者信息
König Patrick, Fiebig Anne, Münch Thomas, Grüning Björn, Scholz Uwe
机构信息
Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, 06466, Germany.
Bioinformatics Group, University of Freiburg, Freiburg im Breisgau, 79098, Germany.
出版信息
Bioinform Adv. 2024 Nov 22;4(1):vbae185. doi: 10.1093/bioadv/vbae185. eCollection 2024.
MOTIVATION
The Galaxy workflow system is an open-source platform supporting data-intensive research in life sciences, featuring a user-friendly web interface for complex analyses without extensive programming. It also offers a representational state transfer based API, enabling remote execution of specific tools. Galaxy supports similarity searches for nucleotide and amino acid sequences, with integrated tools like NCBI BLAST+ and DIAMOND. However, no specialized software currently exists for convenient use of NCBI BLAST+ and DIAMOND via the Galaxy API.
RESULTS
blast2galaxy is a Python package that uses the Galaxy API to run sequence alignments with NCBI BLAST+ and DIAMOND as Galaxy-wrapped tools on compatible servers. It includes a command-line interface that mirrors the CLI of BLAST+ and DIAMOND and a high-level Python API for direct alignments from Python applications. The package relies on bioblend for communication with the Galaxy API.
AVAILABILITY AND IMPLEMENTATION
blast2galaxy is available as open-source software under the MIT license. The source code is available on Github: https://github.com/IPK-BIT/blast2galaxy. It can be installed from the Python Package Index using "pip install blast2galaxy" or from the Bioconda channel using "conda install -c bioconda blast2galaxy". Docker and Apptainer images are available and referenced in the documentation which is available under https://blast2galaxy.readthedocs.io.
动机
Galaxy工作流系统是一个支持生命科学领域数据密集型研究的开源平台，其特点是拥有用户友好的网络界面，可进行复杂分析而无需大量编程。它还提供基于代表性状态转移的应用程序编程接口（API），支持特定工具的远程执行。Galaxy支持对核苷酸和氨基酸序列进行相似性搜索，并集成了如NCBI BLAST+和DIAMOND等工具。然而，目前还没有专门的软件可通过Galaxy API方便地使用NCBI BLAST+和DIAMOND。
结果
blast2galaxy是一个Python包，它使用Galaxy API在兼容服务器上以Galaxy包装工具的形式运行与NCBI BLAST+和DIAMOND的序列比对。它包括一个模仿BLAST+和DIAMOND命令行界面的命令行界面，以及一个用于从Python应用程序直接进行比对的高级Python API。该包依赖bioblend与Galaxy API进行通信。
可用性和实现方式
blast2galaxy作为开源软件，遵循MIT许可协议。源代码可在Github上获取：https://github.com/IPK-BIT/blast2galaxy。可以使用“pip install blast2galaxy”从Python包索引中安装，或使用“conda install -c bioconda blast2galaxy”从Bioconda渠道安装。文档中提供了Docker和Apptainer镜像的相关信息，文档链接为https://blast2galaxy.readthedocs.io 。
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