cirrocumulus 安装说明

zhanglu

参考文档：https://cirrocumulus.readthedocs.io/en/latest/installation.html
安装方式有两种

pip install cirrocumulus
cirro launch <path_to_dataset>

serve方式
先安装mongo
mongod.conf

# 数据库存储路径
dbpath=/data/mongo/data
 
# 日志文件路径
logpath=/data/mongo/logs/mongod.log
 
# 监听的端口
port=27017
 
# 允许所有的 IP 地址连接
bind_ip=0.0.0.0
 
# 启用日志记录
journal=true
 
# 是否后台运行
fork=true
 
# 启用身份验证
#auth=true

docker run -d
-p 27017:27017
-v /data/mongo/config/mongod.conf:/etc/mongod.conf
-v /data/mongo/data:/data/db
-v /data/mongo/logs:/var/log/mongodb
dockerproxy.net/library/mongo:latest

创建数据集
db.createCollection("cirrocumulus")

cirro serve --bind 0.0.0.0:5000 --db_uri mongodb://172.17.0.1:27017/cirrocumulus --upload /home/genostack/workspace/bbbbb/data

curl http://192.168.0.143:5000/api/dataset -X POST -F 'name=my_name' -F 'url=/home/genostack/workspace/bbbbb/cumulus_output.GRCh38-rna.cirro' -F 'description=my_desc' -F 'species=Mus musculus'

zhanglu

cirro docker安装命令

docker run -p 5000:5000 -v /home/genostack:/home/genostack -e "DB_URI=mongodb://172.17.0.1:27017/cirrocumulus" -it dockerhub.genostack.com:8090/library/cirrocumulus:latest

zhanglu

FROM dockerproxy.net/library/python:3.6
ENV PYTHONDONTWRITEBYTECODE=1
ENV PYTHONUNBUFFERED=1
RUN python -m pip install --upgrade pip && python -m pip install cirrocumulus
EXPOSE 5000
ENTRYPOINT ["cirro","serve","--bind","0.0.0.0:5000","--db_uri","mongodb://172.17.0.1:27017/cirrocumulus"]

zhanglu

@zhanglu dockerhub.genostack.com:8090/library/mongo:latest