Metadata-Version: 2.1
Name: DNBC4_test
Version: 1.0.1
Summary: DNBC4 scRNA QC
Home-page: https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software
Author: lishuangshuang3
Author-email: lishuangshuang3@mgi-tech.com
License: UNKNOWN
Description: # DNBelab_C_Series_HT_scRNA-analysis-software
        An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
        ## Introduction
        - **Propose**
          - An open source and flexible pipeline to analyze DNBelab C Series<sup>TM</sup> single-cell RNA datasets. 
        - **Language**
          - Workflow Description Language (WDL), Python3 and R scripts.
        - **Hardware/Software requirements** 
          - x86-64 compatible processors.
          - require at least 50GB of RAM and 4 CPU. 
          - centos 7.x 64-bit operating system (Linux kernel 3.10.0, compatible with higher software and hardware configuration). 
        - **Workflow**
        ![](https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software/blob/master/doc/fig/workflow.jpg)
        ## Directory contents
        - **config**     Read structure configure files
        - **database**   database include fasta,gtf,star index
        - **scripts**    Miscellaneous scripts
        - **software**   Software required in the process
        - **workflows**  WDL pipeline
        ## Installation
        installation manual [here](./doc/installation.md)
        ## Software
        - [PISA](https://github.com/shiquan/PISA)
        - [STAR](https://github.com/alexdobin/STAR)
        ## Database
        Creat database manual [here](./doc/database.md)
        ## config JSON file
        An config JSON file includes all input parameters and genome reference index directory for running pipelines. Always use absolute paths in config JSON.
        <br /> [config JSON file specification](./doc/input_json.md)
        ## Start
        - Setup configure file.
        <br /> Copy [config.json](./example/config.json) from the **example** to the analysis directory and replace it with the real path and fastq path. 
        <br /> Copy [run.sh](./example/run.sh) from the **example** to the analysis directory and replace it with the real path.
        - Run the pipeline
        ```
        ### run the pipeline
        sh run.sh
        ### Background run the pipeline
        nohup sh run.sh > run.log 2>&1 &
        ### run in Cluster(sge)
        echo "sh run.sh" | qsub -cwd -l vf=50G,num_proc=4 -q xxx -N scRNA_run
        ### run in Cluster(pbs)
        echo "sh run.sh" | qsub -d $(pwd) -l nodes=1:ppn=6 -q xxx -N scRNA_run
        ```
        ## FAQ
        Frequently Asked Questions [here](./doc/faq.md)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
