差分

このページの2つのバージョン間の差分を表示します。

--- mitosearch本番環境構築手順 [2024/03/29 00:58] – 210.137.33.14
+++ mitosearch本番環境構築手順 [Unknown date] (現在) – 削除 - 外部編集 (Unknown date) 127.0.0.1
@@ 行 1: / 行 1: @@
-# m128mにmitosearch本番サーバを稼働させる手順
-user2で実行させる
-まだnodejsをインストールしていなければ
-```
-sudo dnf install nodejs -y
-```
-MitoSearchのインストールおよび起動
-```
-cd /suikou/download9-v251/mitosearch
-git clone https://github.com/suikoucalender/mitosearch.git
-cd mitosearch/Mitosearch
-nano config/config.json
-#"port": "3004"に変更 devなら3003、本番環境なら3004
-npm start
-```
-foreverの登録
-```
-sudo npm install -g forever
-logdir=/data/suikou-m2/download9-v251/mitosearch/mitosearch
-workdir=/data/suikou-m2/download9-v251/mitosearch/mitosearch/Mitosearch
-forever start -l $logdir/forever.log -a -o $logdir/out.log -e $logdir/err.log -w --workingDir $workdir --watchDirectory $workdir $workdir/app.js
-```
-起動しているかの確認
-```
-forever list
-#止めるときはforever listで出てきたpidを引数に
-forever stop <pid>
-#もしくは
-forever stopall
-```
-## foreverをsystemdでOS起動時に自動起動させる
-```
-#/etc/systemd/system/mitosearch.service に下記のファイルを作る
-[Unit]
-Description = mitosearch
-After = netwark.target
-[Service]
-Environment=logdir=/data/suikou-m2/download9-v251/mitosearch/mitosearch
-Environment=workdir=/data/suikou-m2/download9-v251/mitosearch/mitosearch/Mitosearch
-ExecStart=/usr/local/bin/forever start -a -l ${logdir}/forever.log -o ${logdir}/out.log -e ${logdir}/err.log -w --workingDir ${workdir} --watchDirectory ${workdir} ${workdir}/app.js
-ExecStop=/usr/local/bin/forever stop ${workdir}/app.js
-Restart=always
-RestartSec=10
-User=user2
-Environment=PATH=/usr/bin:/usr/local/bin
-SyslogIdentifier=node-server
-Type=forking
-Environment=NODE_ENV=production
-[Install]
-WantedBy=multi-user.target
-```
-```
-systemctl daemon-reload #必要に応じて
-systemctl start mitosearch
-systemctl status mitosearch
-systemctl enable mitosearch
-#起動しているかの直接の確認は
-lsof -i:3004 #でポート番号から調べられる
-```
-# mitosearch_devのセットアップ
-```
-#user2で
-cd /suikou/download9-v251/mitosearch
-git clone https://github.com/suikoucalender/mitosearch.git mitosearch_dev
-#yoshitakeやsuikouユーザで
-sudo nano /etc/systemd/system/mitosearch_dev.service
-```
-```
-[Unit]
-Description = mitosearch_dev
-After = netwark.target
-[Service]
-Environment=logdir=/data/suikou-m2/download9-v251/mitosearch/mitosearch_dev
-Environment=workdir=/data/suikou-m2/download9-v251/mitosearch/mitosearch_dev/Mitosearch
-ExecStart=/usr/local/bin/forever start -a -l ${logdir}/forever.log -o ${logdir}/out.log -e ${logdir}/err.log -w --workingDir ${workdir} --watchDirectory ${workdir} ${workdir}/app.js
-ExecStop=/usr/local/bin/forever stop ${workdir}/app.js
-Restart=always
-RestartSec=10
-User=user2
-Environment=PATH=/usr/bin:/usr/local/bin
-SyslogIdentifier=node-server
-Type=forking
-Environment=NODE_ENV=production
-[Install]
-WantedBy=multi-user.target
-```
-```
-sudo systemctl enable --now mitosearch_dev
-```
-# metasearchのセットアップ
-```
-#user2で
-mkdir /suikou/download9-v251/metasearch
-cd /suikou/download9-v251/metasearch
-git clone https://github.com/suikoucalender/metasearch.git
-cd metasearch/metasearch
-npm install
-nano config/config.json
-#passを"pass": "uE7dOLCbHi"
-cd script
-wget https://github.com/suikoucalender/metasearch/releases/download/0.1/krona_v2.7.1_cv1.sif
-wget https://github.com/suikoucalender/metasearch/releases/download/0.1/python3_env_mako_installed.sif
-wget https://github.com/suikoucalender/mitosearch_related_files/releases/download/0.01/ncbi_blast_2.13.0.sif
-mkdir ../data
-cd ../data
-ln -s /suikou/download9-v251/backup-m50v251n3/usr/local/yoshitake/* .
-#yoshitakeやsuikouユーザで
-sudo nano /etc/systemd/system/metasearch.service
-```
-```
-[Unit]
-Description = metasearch
-After = netwark.target
-[Service]
-Environment=logdir=/suikou/download9-v251/metasearch/metasearch
-Environment=workdir=/suikou/download9-v251/metasearch/metasearch/metasearch
-ExecStart=/usr/local/bin/forever start -a -l ${logdir}/forever.log -o ${logdir}/out.log -e ${logdir}/err.log -w --workingDir ${workdir} --watchDirectory ${workdir} ${workdir}/app.js
-ExecStop=/usr/local/bin/forever stop ${workdir}/app.js
-Restart=always
-RestartSec=10
-User=user2
-Environment=PATH=/usr/bin:/usr/local/bin
-SyslogIdentifier=node-server
-Type=forking
-Environment=NODE_ENV=production
-[Install]
-WantedBy=multi-user.target
-```
-```
-sudo systemctl enable --now metasearch
-```
-# metasearch_devのセットアップ
-```
-#user2で
-mkdir /suikou/download9-v251/metasearch
-cd /suikou/download9-v251/metasearch
-git clone https://github.com/suikoucalender/metasearch.git metasearch_dev
-cd metasearch_dev/metasearch
-npm install
-nano config/config.json
-#passを"pass": "uE7dOLCbHi"
-#portを3000->3002
-"urlをhttps://meta.fs.a.u-tokyo.ac.jp/metasearch->https://meta.fs.a.u-tokyo.ac.jp/metasearch_dev
-cd script
-wget https://github.com/suikoucalender/metasearch/releases/download/0.1/krona_v2.7.1_cv1.sif
-wget https://github.com/suikoucalender/metasearch/releases/download/0.1/python3_env_mako_installed.sif
-wget https://github.com/suikoucalender/mitosearch_related_files/releases/download/0.01/ncbi_blast_2.13.0.sif
-#nano config.sh
-##blastdb_pathを編集
-mkdir ../data
-cd ../data
-cp -r /home/yoshitake.kazutoshi/work3/metasearch/2023/db4-2-merge/merge2 db_merge
-mkdir db
-cd db
-for i in `ls ../db_merge/`; do echo $i; j=`basename $i .tsv`; mkdir -p $j; awk -F'\t' -v dir=$j '$1=="id"{filename=dir"/"$2".input"} {print $0 > filename}' ../db_merge/$i ; done
-cd ..
-mkdir blastdb
-ln -s /suikou/download9-v251/metasearch/data/mergedDB.maskadaptors.fa* blastdb/
-ln -s /suikou/download9-v251/metasearch/data/sra_result_2024_01-19.csv.tsv3 sra_info.txt
-#yoshitakeやsuikouユーザで
-sudo nano /etc/systemd/system/metasearch_dev.service
-```
-```
-[Unit]
-Description = metasearch_dev
-After = netwark.target
-[Service]
-Environment=logdir=/suikou/download9-v251/metasearch/metasearch_dev
-Environment=workdir=/suikou/download9-v251/metasearch/metasearch_dev/metasearch
-ExecStart=/usr/local/bin/forever start -a -l ${logdir}/forever.log -o ${logdir}/out.log -e ${logdir}/err.log -w --workingDir ${workdir} --watchDirectory ${workdir} ${workdir}/app.js
-ExecStop=/usr/local/bin/forever stop ${workdir}/app.js
-Restart=always
-RestartSec=10
-User=user2
-Environment=PATH=/usr/bin:/usr/local/bin
-SyslogIdentifier=node-server
-Type=forking
-Environment=NODE_ENV=production
-[Install]
-WantedBy=multi-user.target
-```
-```
-sudo systemctl enable --now metasearch_dev
-```
-# m128mでapacheのインストール
-m128mで稼働させたいサービス
-- mitosearch
-- metasearch
-- let's encrypt
-- mitosearchデータ更新用
-- データバックアップ用
-## apacheのインストール
-```
-sudo dnf install httpd
-```
-```
-sudo nano /etc/httpd/conf.d/proxy.conf
-ProxyPass /metasearch/  http://localhost:3000/
-ProxyPassReverse /metasearch/ http://localhost:3000/
-ProxyPass /metasearch_dev/ http://localhost:3002/
-ProxyPassReverse /metasearch_dev/ http://localhost:3002/
-ProxyPass /mitosearch_dev/ http://localhost:3003/
-ProxyPassReverse /mitosearch_dev/ http://localhost:3003/
-ProxyPass /mitosearch/ http://localhost:3004/
-ProxyPassReverse /mitosearch/ http://localhost:3004/
-ProxyPass /mitosearch_private/ http://localhost:3006/
-ProxyPassReverse /mitosearch_private/ http://localhost:3006/
-```
-```
-sudo systemctl start httpd.service
-sudo systemctl status httpd.service
-sudo systemctl enable httpd.service
-#dummyページ作成
-sudo touch /var/www/html/index.html
-```
-## certbotのインストール
-```
-sudo ln -s /var/lib/snapd/snap /snap
-sudo snap install --classic certbot
-#m50v251n3から/etc/letsencrypt/をコピーしておく。シンボリックリンクはシンボリックリンクでコピーする必要があるようなので、tarで固めてからコピーした。
-echo '<VirtualHost *:80>
-  DocumentRoot "/var/www/html"
-  ServerName "meta.fs.a.u-tokyo.ac.jp"
-</VirtualHost>
-' >> /etc/httpd/conf/httpd.conf
-sudo yum -y install mod_ssl
-certbot --apache
-#これでhttpsがつながるようになる
-#更新のテスト
-/var/lib/snapd/snap/bin/certbot renew --dry-run --post-hook "systemctl restart httpd.service"
-#cronに下記を登録
-/var/lib/snapd/snap/bin/certbot renew --post-hook "systemctl restart httpd.service"
-```
-## r251→m50v251n3のhttp, httpsをr251→m128mに切り替える
-```
-ssh -l yoshitake r251
-sudo nano /etc/ufw/before.rules
-#下記に変更
-#-A PREROUTING -i enp5s0 -p tcp -d 133.11.144.11 --dport 80 -j DNAT --to-destination 192.168.253.160:80
-#-A PREROUTING -i enp5s0 -p tcp -d 133.11.144.11 --dport 443 -j DNAT --to-destination 192.168.253.160:443
-sudo systemctl restart ufw.service
-```
-# データベースの自動更新スクリプトの定期実行
-user2で
-```
-cd /suikou/download9-v251/mitosearch_update
-git clone https://suikoucalender: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@github.com/suikoucalender/mitosearch_related_files
-```
-# crontabでの自動実行
-```
-#m128m
-4 * * * root rsync -av --progress --delete m32s:/m2/db m32s:/m2/download m32s:/m2/download9 m32s:/m2/tool m32s:/m2/tool9 m32s:/m2/tool-all m32s:/m2/tool9-all /data/suikou-m2/
-#0 6 * * * yoshitake.kazutoshi rsync -av --progress --delete /suikou/download9-v251 /suikou/root-files-v251 r251:/data/backup-m128m
-0 1 * * user2 bash /suikou/download9-v251/mitosearch_update/mitosearch_related_files/script/mitosearch_db.sh > /tmp/mitosearch_db_$(date "+\%Y\%m\%d-\%H\%M").log 2>&1
-3 * * 6 root /var/lib/snapd/snap/bin/certbot renew --post-hook "systemctl restart httpd.service" > /tmp/letsencrypt_$(date "+\%Y\%m\%d-\%H\%M").log 2>&1
-```
-```
-#m30v251n3
-6 * * * root rsync -av --progress --delete m128m:/data/suikou-m2/root-files-v251 m128m:/data/suikou-m2/download9-v251 /mnt/n3data/backup-m128m
-```