pybrave 0.1.9

Bioinformatics Reactive Analysis and Visualization Engine

Bioinformatics Reactive Analysis and Visualization Engine

Installation

pip install pybrave

Usage

brave

• http://localhost:5000

install pipeline

git clone https://github.com/pybrave/pipeline-metagenomics.git ~/.brave/pipeline/7530139e-8985-423f-9fb6-32650828ca40

brave --base-dir /ssd1/wy/workspace2/nextflow_workspace \
    --work-dir /data/wangyang/nf_work \
    --pipeline-dir /ssd1/wy/workspace2/nextflow-fastapi/pipeline-dev \
    --literature-dir /ssd1/wy/workspace2/nextflow-fastapi/literature \
    --db-type mysql --mysql-url root:123456@192.168.3.60:53306/pipeline  \
    --port 5000

docker

mkdir $PWD/data
docker run --rm -p 5000:5000  \
  --user $(id -u):$(id -g) \
  -v  /var/run/docker.sock:/var/run/docker.sock  \
  -v /tmp/brave.sock:/tmp/brave.sock \
  -v $PWD/data:/.brave \
  registry.cn-hangzhou.aliyuncs.com/wybioinfo/pybrave

git clone https://github.com/pybrave/pipeline-metagenomics.git  $PWD/data/pipeline/7530139e-8985-423f-9fb6-32650828ca40

docker run --rm -p 5000:5000  \
  --user $(id -u):$(id -g) \
 --group-add $(stat -c '%g' /var/run/docker.sock) \
  -v  /var/run/docker.sock:/var/run/docker.sock  \
  -v /tmp/brave.sock:/tmp/brave.sock \
  -v ~/.brave:/.brave \
  -v /ssd1:/ssd1 \
  -v /data:/data \
  registry.cn-hangzhou.aliyuncs.com/wybioinfo/pybrave \
  brave --pipeline-dir /ssd1/wy/workspace2/nextflow-fastapi/pipeline-dev \
  --base-dir /ssd1/wy/workspace2/nextflow_workspace \
  --work-dir /data/wangyang/nf_work \
  --literature-dir /ssd1/wy/workspace2/nextflow-fastapi/literature \
  --db-type mysql \
  --mysql-url root:123456@192.168.3.60:53306/pipeline \
  --port 5000 

development

mkdir -p development/pipeline-dev
mkdir -p development/base-dev 
python  -m brave \
   --port 5000 \
   --pipeline-dir development/pipeline-dev \
   --base-dir development/base-dev 
git clone https://github.com/pybrave/pipeline-metagenomics.git  development/pipeline-dev/7530139e-8985-423f-9fb6-32650828ca40

contact

• [e-mail]