目录
- .githubUpdate GitHub Actions workflow to streamline Python setup and distribution process, including upgrading action versions and changing Python version to 3.10.2个月前
- cgatcoreFix signal handler flood: guard against worker processes at fire time1个月前
- condamerge master1年前
- docsUpdate documentation to reflect current codebase1个月前
- scriptspep84年前
- testsUpdate test_slurm_job_monitoring for new squeue->sacct flow1个月前
- .codecov.ymlHave added Coverage tests1年前
- .gitignoreincluded S3 decorators1年前
- CHANGELOG.mdUpdate executor docs and CHANGELOG for 0.6.211个月前
- Dockerfile[AH} fix miniconda path6年前
- INSTALL{AH,SLV,AC} first import8年前
- KNOWN_BUGS{AH,SLV,AC} first import8年前
- LICENSEFinished project_info1年前
- MANIFEST.in{AH} change CGATCore to cgatcore7年前
- README.mdHave added Coverage tests1年前
- THANKS.txt include thanks.txt8年前
- all-tests.shNow included --local for testing the pipelines since there is no cluster.1年前
- conda_requires.txtadd missing conda deps3年前
- install.sh[AH} fix miniconda path6年前
- mkdocs.ymlUpdate mkdocs.yml to change 'rendering' to 'options' for Python handler configuration.2个月前
- pyproject.tomlBump version to 0.6.221个月前
- requirements.txtremove function remote_file_exists, removes paramiko dependency4年前
- setup.cfgfix pycodestyle1年前
- setup.pyadded pyproject.toml1年前
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CGAT-core
CGAT-core is a workflow management system that allows users to quickly and reproducibly build scalable data analysis pipelines. CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.
Documentation for CGAT-core can be accessed here
CGAT-core is open-sourced, powerful and user-friendly, and has been continually developed as a Next Generation Sequencing (NGS) workflow management system over the past 10 years.
Installation
The following sections describe how to install the cgatcore framework.
The preferred method to install the cgatcore is using conda, by following the instructions on read the docs. However, there are a few other methods to install cgatcore, including pip and our own bash script installer.