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gzy
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public/scripts/complete loading.sh
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208
public/scripts/complete loading.sh
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# 创建共用网络
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docker network create media-network
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# 运行数据库容器
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# docker run --name mediaMysql \
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# --network media-network \
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# -p 3306:3306 \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/data/:/var/lib/mysql \
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# -e MYSQL_ROOT_PASSWORD='Gzy1234566.' \
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# -d my-media-mysql:v1
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/mysql/data/:/var/lib/mysql \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/mysql/conf:/etc/mysql/conf.d \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/log/:/var/log/mysql \
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# docker volume create media-mysql-data
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docker run --name mediaMysql \
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--network media-network \
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-e MYSQL_ROOT_PASSWORD='Gzy1234566.' \
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-v media-mysql-data:/var/lib/mysql \
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-p 3306:3306 \
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-d \
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media-mysql:v1 \
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mysqld
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docker exec -it mediaMysql mysql -uroot -p
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Gzy1234566.
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# CREATE TABLE cultured_data (
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# `id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY COMMENT 'Primary key',
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# `species_dive_id` INT NOT NULL COMMENT 'species dive id',
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# `pH` TEXT NULL COMMENT 'pH',
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# `o2` TEXT NULL COMMENT 'o2',
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# `microbial_name` TEXT NULL COMMENT 'species name',
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# `media_name` TEXT NULL COMMENT 'media name',
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# `media_source` TEXT NULL COMMENT 'media source',
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# `mediadive_id` TEXT NULL COMMENT 'mediadive id',
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# `nutrition` TEXT NULL COMMENT 'compounds list',
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# `gram_stain` TEXT NULL COMMENT 'gram type',
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# `temperature` TEXT NULL COMMENT 'temperature',
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# `domain` TEXT NULL COMMENT 'domain',
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# `phylum` TEXT NULL COMMENT 'phylum',
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# `class` TEXT NULL COMMENT 'Class',
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# `order` TEXT NULL COMMENT 'order',
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# `family` TEXT NULL COMMENT 'family',
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# `genus` TEXT NULL COMMENT 'genus',
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# `species` TEXT NULL COMMENT 'species',
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# `taxonomy` TEXT NULL COMMENT 'taxonomy',
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# `synonym` TEXT NULL COMMENT 'synonym',
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# `genome` VARCHAR(50) NULL COMMENT 'genome',
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# `predict_temperature` TEXT NULL COMMENT 'predict temperature',
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# `predict_pH` TEXT NULL COMMENT 'predict pH',
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# `predict_o2` TEXT NULL COMMENT 'predict o2',
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# `cultured_type` TEXT NULL COMMENT 'culture type'
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# ) COMMENT 'Cultured microbial data';
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# `genome` VARCHAR(50) NULL COMMENT 'genome',
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# `genome` TEXT NULL COMMENT 'genome',
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# 赋予可读权限
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# chown mysql:mysql /var/lib/mysql-files/cultured_dataLinux.csv
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# chmod 644 /var/lib/mysql-files/cultured_dataLinux.csv
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# LOAD DATA INFILE '/var/lib/mysql-files/cultured_dataLinux.csv'
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# INTO TABLE cultured_data
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# FIELDS TERMINATED BY ','
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# OPTIONALLY ENCLOSED BY '"'
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# LINES TERMINATED BY '\n'
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# IGNORE 1 ROWS
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# (species_dive_id,pH,o2,microbial_name,media_name,media_source,mediadive_id,nutrition,gram_stain,temperature,domain,phylum,Class,`order`,family,genus,species,taxonomy,synonym,genome,predict_temperature,predict_pH,predict_o2,cultured_type);
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# UPDATE cultured_data
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# SET cultured_type = REPLACE(REPLACE(REPLACE(cultured_type, '\t', ''), '\r', ''), '\n', '');
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# UPDATE cultured_data
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# SET predict_o2 = 'aerobe'
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# WHERE predict_o2 = 'aerotolerant';
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# UPDATE cultured_data
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# SET phylum = 'Thermotogota'
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# WHERE phylum = 'Thermotogae';
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# UPDATE cultured_data
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# SET phylum = 'Aquificota'
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# WHERE phylum = 'Aquificae';
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# UPDATE cultured_data
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# SET phylum = 'Thermodesulfobacteriales'
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# WHERE phylum = 'Thermodesulfobacteria';
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# UPDATE cultured_data
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# SET class = 'Actinomycetes'
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# WHERE class = 'Actinobacteria';
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# 运行Web服务器容器
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docker run -d \
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--name mediaNode \
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--network media-network \
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-p 3000:3000 \
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-v /var/run/docker.sock:/var/run/docker.sock \
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-v /usr/bin/docker:/usr/bin/docker \
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-v /vol1/1000/home/gzy/mediaDatabase/media-transformer/:/app \
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-w /app \
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media-node:v2 \
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nodemon server.js
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docker exec -it mediaNode bash
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npm install -g nodemon
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# # prokka容器
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# docker run -it --name prokka \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/:/app/ \
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# -w /app \
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# media-prokka:v1 \
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# bash
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# ./prokka_batch.sh --input /app/input_data --output /app/output_results --threads 4 --force
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# pH预测容器运行测试
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# docker run --rm \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
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# -w /app \
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# ph-pred:v4 \
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# bash -c "conda run -n ph_model_jupyter bash /app/scripts/pHPredict.sh /app/prokka_annotation /app/results/ph_predict"
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# docker run -d \
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# --name phpredict \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
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# -w /app \
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# media-ph-pred:v1 \
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# tail -f /dev/null
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# docker exec -it phpredict bash
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# 温度氧气预测容器运行测试
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# docker run --rm \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
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# -w /app \
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# bacdive-ai:v1 \
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# bash -c "source /etc/profile && source /opt/conda/etc/profile.d/conda.sh && conda activate bacdiveai && pip install --root-user-action=ignore tqdm && bash /app/scripts/TempO2Predict.sh /app/prokka_annotation /app/results/tempo2predict"
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# docker run -d \
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# --name tempo2predict \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
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# -w /app \
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# bacdive-ai:v1 \
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# tail -f /dev/null
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# docker exec -it tempo2predict bash
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# 最大生长速率预测容器运行测试
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# docker run --rm \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
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# -w /app \
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# shengwei/grodon2:latest \
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# bash -c "bash /app/scripts/GrowthPredict.sh /app/prokka_annotation /app/results/growth_predict"
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# docker run -d \
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# --name growthpredict \
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# -e PATH='/usr/local/bin:/usr/bin:/bin:/opt/conda/lib/R/bin' \
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# -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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# -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
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# -w /app \
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# media-grodon2:v1 \
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# tail -f /dev/null
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# docker exec -it growthpredict bash
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# 远程调用GPU服务器进行培养基预测
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# 将用户加入doker用户组
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sudo usermod -aG docker gzy
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# 检查是否安装nvidia-docker2
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docker run --rm \
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-v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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-v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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-v "/vol1/1000/home/gzy/mediaDatabase/mediaTransformer":/app/scripts \
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-w /app \
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media-trasnformer:v2 \
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bash -c "source /opt/conda/etc/profile.d/conda.sh && conda activate uncultured_pytorch && pip install sentencepiece && bash /app/scripts/mediaPredict.sh /app/prokka_annotation /app/results/media_predict"
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docker run -d \
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--name mediapredict \
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-v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
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-v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
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-v "/vol1/1000/home/gzy/mediaDatabase/mediaTransformer":/app/scripts \
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-w /app \
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media-trasnformer:v2 \
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tail -f /dev/null
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docker exec -it mediapredict bash
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