USAIL: a user-centric, scalable and interactive tool for large-scale single-cell RNA-seq data analysis
**USAIL** is a user-centric, scalable, and interactive tool designed for large-scale single-cell RNA-seq (scRNA-seq) data analysis. Utilizing Apache Spark, it accelerates the data processing for scRNA-seq data.Furthermore, USAIL provides a wide array of downstream analysis modules, such as gene set enrichment and cell-cell interaction analysis. A unique feature of USAILscRNA is its user-centric case studies, designed according to the major applications of scRNA-seq in medical and biological research, such as cancer, development, and infectious disease. These case studies guide researchers in selecting appropriate tools, enabling them to focus on biological insights rather than computational foundations.
- Linux
- Windows
- Docker
- Docker compose
We have packaged all of our interactive programs and computational procedures into the following two compressed files.
- fastq_scsparkstarsolo_tlinux3.2
- fastq_scspark_tlinux3.2
- cirrocumulus
- single_cell_analysis:1.4.5.0
- single_cell_server.tgz : It includes one docker image used for interactive parameter selection in the single-cell analysis workflow.
- Download the necessary files and Pull the required images.
mkdir usail/
cd ./usail
wget https://github.com/xmuyulab/USAIL-XMBD/raw/main/single_cell_server.tgz
tar -xzvf single_cell_server.tgz
docker pull liangcy98/fastq_scsparkstarsolo_tlinux3.2:v1
docker pull liangcy98/fastq_scspark_tlinux3.2:v1
docker pull liangcy98/cirrocumulus:latest
docker pull liangcy98/single_cell_analysis:1.4.5.0
docker pull liangcy98/single_cell_backend:latest
docker pull liangcy98/single_cell_frontend:latest
docker pull liangcy98/single_cell_redis:latest
- Start Docker
docker-compose up -d- 本地浏览器进入交互式页面端：[服务器IP]:8080
# If the server IP is 10.24.80.102, then enter it into the local browser.
http://10.24.80.102:8080/
- Upload data & Choose paremeter & Data processing
- Then copy the following command, then paste and run it in Docker Terminal.
docker run --rm --name admin_20230825_033529_81764_0_16490 -v $(pwd)/server/result/admin/PreProcessing:/Input:rw -v $(pwd)/server/result/admin/20230825_033529_81764_0:/Output:rw -v $(pwd)/server/algorithm_platform:/algorithm:rw liangcy98/single_cell_analysis:1.4.5.0 bash -c "cd /algorithm/ && bash run_job.sh /Output/file_para.json"- View the execution results.
cd ./server/result/admin/