大服务器服务部署命令清单

zhanglu

服务清单：

nexus:

docker run -d --network=host -v /ceph_disk2/app/nexus:/nexus-data sonatype/nexus3

nodebb:

su nodebb
cd /ceph_disk3/nodebb/NodeBB-1.13.4-5
./start.sh

jupyter:

部署在k8s: 不用手动启动

postgres:

docker run  -v /ceph_disk2/data/hongyuan/data/postgresql_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres_anneng@8425# -p 5435:5432 -d postgres:10

redis:

systemctl start redis

cromwell:

cd /data_raid1/bioinfo/app/cromwell
sudo ./start_cromwell_local.sh

harbor: anneng 用户

/home/anneng/app/harbor/install.sh

gitlab:

docker run \
-itd \
-p 9880:9880 \
-p 9822:22 \
-v /data_raid1/gitlab/etc:/etc/gitlab \
-v /data_raid1/gitlab/log:/var/log/gitlab \
-v /data_raid1/gitlab/opt:/var/opt/gitlab \
--privileged=true \
twang2218/gitlab-ce-zh:latest

zhanglu

查看pod
kubectl get pod -n rook-ceph
kubectl exec -it rook-ceph-tools-6cccf8dc7b-69tlf bash -n rook-ceph

查看副本数
ceph osd pool get myfs-data0 size
ceph osd pool get myfs-metadata size

rook-ceph修改副本数
ceph osd pool set myfs-data0 size 1 --yes-i-really-mean-it
ceph osd pool set myfs-metadata size 1 --yes-i-really-mean-it

zhanglu

EDNA
cd /data_raid1/genostack_v3/genostack_tool/analysis_16s_project2
./start.sh
cd /data_raid1/genostack_v3/genostack_tool/analysis_16s
./start.sh

ice-melt

分子遗传标记

docker重装过,目前使用root启动
cd /ceph_disk3/lx/services/angs_molecular_genetic_analysis && ./start.sh

zhangfanglin

诺如病毒：项目

打包以及启动地址： /var/www/html/docker_app/Norovirus_typing  && vi build.sh
docker run -itd --name=norovirus_typing -p 100:80 dockerhub.genostack.com:8090/library/norovirus_typing:V0.6 /bin/bash

RStudio --工具

打包以及启动地址： /var/www/html/docker_app/RStudio && vi start.sh   build.sh
docker run -itd --network host  -v /var/www/html/docker_app/RStudio/www:/usr/lib/rstudio-server/www \
        -v /var/www/html/docker_app/RStudio/database.conf:/etc/rstudio/database.conf \
        -v /var/www/html/docker_app/RStudio/anneng:/home/anneng dockerhub.genostack.com:8090/library/r_studio:V0.3

CKAN 文件管理

本地打包地址：/work/project/genostack_all/genostack_app/ckan
线上启动地址：/var/www/html/docker_app/ckan

docker run --name ckan-solr -p 8983:8983 -d ckan/ckan-solr:2.10-solr9

#  ckan -c /etc/ckan/default/ckan.ini search-index rebuild    --ckan-solr服务停止后需要进入 ckan的服务进行索引处理

docker run  -d -p 8082:8082  -v /var/www/html/docker_app/ckan/nginx_ckan:/etc/nginx/sites-available/ckan -v /var/www/html/docker_app/ckan/ckan.ini:/etc/ckan/default/ckan.ini  -v /cephfs_data/ckan/storage_path:/var/lib/ckan -v /ceph_disk2:/ceph_disk2 dockerhub.genostack.com:8090/library/ckan:V2.10  bash

jbrowse ---工具

打包以及启动地址：/var/www/html/docker_app/jbrowse  
# 占用99端口
docker run  --network=host -d dockerhub.genostack.com:8090/library/jbrowse-web:v2.4.2

jbrowse_an (开发嵌入式版本) ---工具

打包以及启动地址：/var/www/html/docker_app/jbrowse_an

docker run -itd --name=jbrowse_an \
        -v /cephfs_data:/cephfs_data \
        -v /ceph_disk2:/ceph_disk2 \
        -v /data_raid1:/data_raid1 \
        -v /var/www/html/docker_app/jbrowse_an/.env:/var/www/html/api/.env \
        -p 1003:80 dockerhub.genostack.com:8090/library/jbrowse_an:V0.1 /bin/bash

核磁工具--等会验证

本地打包地址：
docker pull dockerhub.genostack.com/angs/nmrium:v01
docker run  -p 87:3000 -d dockerhub.genostack.com/angs/nmrium:v01

q2view --工具

打包以及启动地址：/var/www/html/docker_app/q2view
docker run --network=host -itd  dockerhub.genostack.com:8090/library/q2view:V0.1

rath --工具

打包以及启动地址：/var/www/html/docker_app/rath

docker run -itd --name=rath  -p 6010:3000 dockerhub.genostack.com:8090/library/rath:V0.2 /bin/bash

redash--等会验证

打包以及启动地址：/var/www/html/docker_app/redash

sanshu_database(三黍数据库工具)

打包以及启动地址：/var/www/html/docker_app/sanshu_database
docker run  -itd -p 89:89  dockerhub.genostack.com:8090/library/sanshu_database:V1.4

sanshu_mutant_database(三黍突变体数据库工具)

打包以及启动地址：/var/www/html/docker_app/sanshu_mutant_database
docker run  -itd -p 90:88  dockerhub.genostack.com:8090/library/sanshu_mutant_database:V1

superset --工具

/var/www/html/docker_app/superset

docker run -itd --name=superset --network host  dockerhub.genostack.com:8090/library/superset:V0.1 /bin/bash

vcfiobio --工具

打包以及启动地址：/var/www/html/docker_app/vcfiobio

docker run --network host  -p 9002:9002 -v /data_raid1:/data_raid1 -v /ceph_disk3/lx/temp/instance:/workspace/angs_molecular_genetic_analysis_api/instance -d anneng01:8090/angs/vcf_iobio:latest

webSocket(平台使用)

打包以及启动地址：/var/www/html/docker_app/webSocket

docker run  -v /var/www/html/docker_app/webSocket/.env:/var/www/html/.env -p 6009:6001 -d dockerhub.genostack.com:8090/library/web_socket:latest

genostack(平台)

打包以及启动地址：/var/www/html/docker_app/genostackV3
docker run  --network=host --name=genostackv3 \
        -v /ceph_disk2:/ceph_disk2 \
        -v /data_raid1/bioinfo/app/cromwell:/data_raid1/bioinfo/app/cromwell \
        -v /var/www/html/docker_app/genostackV3/.env:/var/www/html/.env \
        -v /ceph_disk2/data/dock_store_workflow:/var/www/html/genostack_all/qiime2/workflow \
  -d -p 81:81  dockerhub.genostack.com:8090/library/genostack:v3.12.13

blast 序列比对 sequenceserver --工具


docker run --network host  -d \
-v /ceph_disk2/data/hongyuan/mnt/data/public_data/yancao16sampleflashmergeblastnt_1661134479:/db/yancao16sampleflashmerge \
-v /ceph_disk2/data/hongyuan/mnt/data/public_data/Human_pathogen_database_1650333669:/db/human \
-v /ceph_disk2/data/yancao16yangben_flash_blast/T101:/db/T101 \
-v /ceph_disk3/yancao/16_yangben_yancao_blast_db:/db/16_yangben_yancao_blast_db \
-v /ceph_disk2/MetaDatabase/ntdata:/db/nucleotide \
-v /ceph_disk2/data/hongyuan/mnt/data/public_data/tobaccodb16yangben_1658825751:/db/tobaccodb \
-v /var/www/html/sequenceserver/sequenceserver.conf:/root/.sequenceserver.conf wurmlab/sequenceserver

基因表达分析 genecloudomics --工具


docker run  -p 3838:3838 -d jaktab/genecloudomics-webserver /opt/shiny-server/bin/shiny-server

hitom

/var/www/html/hitom
docker run  -v /var/www/html/hitom/data/:/mnt --network host -it  dockerhub.genostack.com/external/hitom:latest /bin/sh

NextStrain （平台使用）工具

项目地址：/var/www/html/auspice
打包：npm run build
rm -rf /var/www/html/docker_app/genostackV3/illumina_genostack/public/auspice
cp -r  /var/www/html/auspice/dist /var/www/html/docker_app/genostackV3/illumina_genostack/public/auspice

IGV工具

打包地址：/ceph_disk3/lx/services/ms_igv 
workdir=/ceph_disk3/lx/services/ms_igv/instance
docker_version=V01.09
# 删除之前历史遗留的日志和无用数据文件(可选)
# sudo rm ${workdir}/log/*
# sudo rm -rf ${workdir}/data_dir/*

# 启动命令
docker run -d \
-p 5002:5000 \
--restart=always \
-v /ceph_disk1:/ceph_disk1 \
-v /ceph_disk2:/ceph_disk2 \
-v /ceph_disk3:/ceph_disk3 \
-v /data_raid1:/data_raid1 \
-v ${workdir}:/workspace/instance \
dockerhub.genostack.com:8090/angs/ms_igv:${docker_version}

ice-melt

aspera 下载

su root
su lx

conda activate angs_api_dwonload
cd /ceph_disk3/lx/app/angs_api_download
./start.sh

zhanglu

@zhanglu
nexus 更新
docker run -d --network=host -v /ceph_disk2/app/nexus:/nexus-data sonatype/nexus3:3.63.0

ice-melt

代码仓库下载


cd  /ceph_disk3/lx/services/repo_downloader
./start.sh

zhanglu

安至项目：

docker run \
 -v /data_raid1/genostack_v3/genostack_base/redis:/data \
  -p 6377:6379 -d redis:latest redis-server

docker run \
 -v /data_raid1/genostack_v3/genostack_base/postgres/:/var/lib/postgresql/data \
  -e POSTGRES_PASSWORD=anneng@1235_Jike2015 -p 5438:5432 -d postgres:10

docker run  -v /var/www/html/webSocket/websocket_env:/var/www/html/.env -p 6002:6001 -d dockerhub.genostack.com:8090/library/web_socket:latest


docker run --name=genostack_anzhi --network=host  \
-v /data_raid1/genostack_v3:/data_raid1/genostack_v3 \
-v /data_raid1/genostack_v3/genostack_core/cromwell/cromwell-executions:/cromwell-executions \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/config/.env:/var/www/html/.env \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/output:/var/www/html/public/output \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/php_sours:/var/www/html/public/php_sours \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/reportHtml:/var/www/html/public/reportHtml \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/wdl:/var/www/html/public/wdl \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/cwl:/var/www/html/public/cwl \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/json:/var/www/html/public/json \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/config/zz-docker.conf:/usr/local/etc/php-fpm.d/zz-docker.conf \
-d dockerhub.genostack.com:8090/library/genostack_php_7_6_cwl:V3.8.11

docker run  \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/config/defaultV3.conf:/etc/nginx/conf.d/default.conf \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/output:/var/www/html/public/output \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/php_sours:/var/www/html/public/php_sours \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/reportHtml:/var/www/html/public/reportHtml \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/wdl:/var/www/html/public/wdl \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/cwl:/var/www/html/public/cwl \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/json:/var/www/html/public/json \
-v /data_raid1/genostack_v3/genostack_core/cromwell/cromwell-executions:/data_raid1/genostack_v3/cromwell/cromwell-executions \
-v /data_raid1/genostack_v3/genostack_core/cromwell/cromwell-executions:/cromwell-executions \
-v /data_raid1/genostack_v3:/data_raid1/genostack_v3 \
-v /data_raid1/genostack_v3/genostack_core/php_nginx/source_v3/favicon.ico:/var/www/html/public/favicon.ico \
-d -p 92:82 dockerhub.genostack.com:8090/library/qiime_nginx:V3.8.11

docker run -p 8011:8000 \
-v /usr/bin/docker:/usr/bin/docker \
-v /var/run/docker.sock:/var/run/docker.sock \
-v /data_raid1/genostack_v3/genostack_core/cromwell/local.conf:/local.conf \
-v /data_raid1/genostack_v3/genostack_core/cromwell/nohup.out:/nohup.out \
dockerhub.genostack.com:8090/library/cromwell:51

zhanglu

edna环境DNA
/data_raid1/genostack_v3/genostack_tool/analysis_16s/start.sh
/data_raid1/genostack_v3/genostack_tool/analysis_16s_project2/start.sh

zhanglu

@zhanglu docker run --restart=always -d
-v /data_raid1/bioinfo/app/cromwell/cromwellstatus_project/application.yml:/application.yml
-v /data_raid1/bioinfo/app/cromwell/nohup.out:/nohup.out
-p 9080:9080 dockerhub.genostack.com:8090/app/cromwellstatus:v1

zhanglu

docker run -p 9081:9081
-v /usr/bin/docker:/usr/bin/docker
-v /var/run/docker.sock:/var/run/docker.sock
-v /ceph_disk2/app/nextflow/genostack_nextflow_api/config/application.yml:/application.yml
-v /ceph_disk2:/ceph_disk2
-v /ceph_disk3:/ceph_disk3
-v /ceph_disk2/app/nextflow/genostack_nextflow_api/plugins:/root/.nextflow/plugins
-d dockerhub.genostack.com:8090/library/nextflowapi:v4.41

zhanglu

@zhanglu /opt/app/genostack_v3_service/genostack_tool/amplicon_analysis_16s.yaml