{"id":2673,"date":"2019-04-01T23:18:03","date_gmt":"2019-04-01T15:18:03","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2673"},"modified":"2023-09-13T15:38:04","modified_gmt":"2023-09-13T07:38:04","slug":"%e4%bd%bf%e7%94%a8sequenceserver%e6%90%ad%e5%bb%ba%e6%9c%ac%e5%9c%b0%e5%8c%96blast%e7%bd%91%e9%a1%b5%e6%9c%8d%e5%8a%a1","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2673","title":{"rendered":"\u4f7f\u7528SequenceServer\u642d\u5efa\u672c\u5730\u5316blast\u7f51\u9875\u670d\u52a1"},"content":{"rendered":"\n

1. \u7b80\u4ecb<\/h1>\n\n\n\n

\u73b0\u5728NCBI\u4e0d\u518d\u63d0\u4f9bwwwblast\u8f6f\u4ef6\u4e0b\u8f7d\u3002\u4e14NCBI\u7684wwwblast\u8f6f\u4ef6\u5f88\u4e45\u6ca1\u66f4\u65b0\uff0c\u754c\u9762\u7b80\u964b\uff0c\u56e0\u6b64\u4e0d\u63a8\u8350\u4f7f\u7528\u8be5\u8f6f\u4ef6\u8fdb\u884c\u672c\u5730\u5316blast\u5206\u6790\u3002\u4f7f\u7528SequenceServer<\/a>\u90e8\u7f72\u672c\u5730\u5316blast\u7f51\u9875\u670d\u52a1\uff0c\u754c\u9762\u7b80\u5355\u6613\u7528\uff0c\u8fd8\u53ef\u4ee5\u540c\u65f6\u52fe\u9009\u591a\u4e2a\u6570\u636e\u5e93\u8fdb\u884c\u6bd4\u5bf9\u5206\u6790\u3002\u4ee5\u4e0b\u8bb2\u89e3\u4f7f\u7528Sequenceserver<\/a>\u5728Rocky 9.2 Linux\u7cfb\u7edf\u4e0a\u642d\u5efa\u672c\u5730\u5316blast\u7f51\u9875\u670d\u52a1\u3002<\/p>\n\n\n\n

2. \u5b89\u88c5\u8f6f\u4ef6<\/h1>\n\n\n\n

\u7531\u4e8eSequenceServer\u8f6f\u4ef6\u91c7\u7528Ruby\u7f16\u7a0b\uff0c\u5176\u90e8\u7f72\u9700\u8981\u5148\u4f7f\u7528root\u7528\u6237\u5b89\u88c5\u6240\u9700\u8981\u4f9d\u8d56\u7684ruby\u8f6f\u4ef6\u3002\u7531\u4e8e\u5f53\u524d\u6700\u65b0\u7248\u672cSequenceSever 2.1.0\u7248\u672c\u7684\u5b89\u88c5\u548c\u4f7f\u7528\u9700\u8981\u4f9d\u8d56\u9ad8\u4e8e3.0.6\u7248\u672c\u7684ruby\u8f6f\u4ef6\uff0c\u800cRocky 9.2\u7cfb\u7edf\u9ed8\u8ba4\u5b89\u88c5\u7684ruby\u8f6f\u4ef6\u7248\u672c\u4e3a3.0.4\uff0c\u4e0d\u80fd\u6ee1\u8db3\u9700\u6c42\u3002\u56e0\u6b64\u9700\u8981\u72ec\u7acb\u5b89\u88c5\u9ad8\u7248\u672c\u7684ruby\u8f6f\u4ef6\u540e\uff0c\u518d\u5b89\u88c5\u6700\u65b0\u7248\u672c\u7684SequenceServer\u8f6f\u4ef6\u3002<\/p>\n\n\n\n

# \u9996\u5148\u4f7f\u7528dnf\u547d\u4ee4\u5b89\u88c5ruby\u548crbenv\u3002\nsudo dnf install ruby ruby-devel rbenv gem\n\n# \u7136\u540e\uff0c\u4f7f\u7528rbenv\u7684ruby-build\u547d\u4ee4\u5b89\u88c5\u9ad8\u7248\u672cruby\u3002\r\nsudo ruby-build --list\r\nsudo ruby-build 3.1.2 \/opt\/sysoft\/ruby-3.1.2\n\n# \u6700\u540e\uff0c\u4f7f\u7528\u9ad8\u7248\u672cruby\u5b89\u88c5sequenceserver\r\nsudo \/opt\/sysoft\/ruby-3.1.2\/bin\/gem install sequenceserver\n\necho 'PATH=\/opt\/sysoft\/ruby-3.1.2\/bin:$PATH' >> ~\/.bashrc\nsource ~\/.bashrc<\/code><\/pre>\n\n\n\n
3. \u4f7f\u7528sequenceserver<\/h1>\n\n\n\n
3.1 \u7b80\u5355\u4f7f\u7528\u65b9\u6cd5<\/h2>\n\n\n\n
\u4f7f\u7528sequenceserver\u8981\u6c42\u5b89\u88c5\u6709NCBI-blast+\u7a0b\u5e8f\u53ca\u5176\u6570\u636e\u5e93\u3002<\/p>\n\n\n\n
# sequenceserver -d \/opt\/biosoft\/wwwblast\/db -n 16 -p 4567\n\u7a0b\u5e8f\u8fd0\u884c\u540e\uff0c\u5728\u672c\u673a\u7684\u6d4f\u89c8\u5668\u4e2d\u6253\u5f00 localhost:4567\uff0c\u5373\u53ef\u8bbf\u95ee\u672c\u5730\u5316blast\u7f51\u9875\u670d\u52a1\u3002\n\n\u5e38\u7528\u53c2\u6570\uff1a\n-b | --bin \n    \u8f93\u5165ncbi-blast+\u7684bin\u6587\u4ef6\u8def\u5f84\n\n-d | --database_dir\n    \u8f93\u5165blast\u6570\u636e\u5e93\u8def\u5f84\n\n-n | --num_threads\n    \u8bbe\u7f6e\u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\n\n-H | --host\r\n    \u8bbe\u7f6e\u8fd0\u884c\u7a0b\u5e8f\u7684\u4e3b\u673a\u4fe1\u606f\uff0c\u9ed8\u8ba4\u4e3alocalhost\uff0c\u5219\u542f\u52a8\u7a0b\u5e8f\u540e\uff0c\u53ef\u4ee5\u5728\u672c\u673a\u4e0a\u8bbf\u95eelocalhost:4567\u3002\u82e5\u9700\u8981\u63d0\u4f9b\u8fdc\u7a0b\u8bbf\u95ee\u670d\u52a1\uff0c\u5219\u9700\u8981\u586b\u5199\u5bf9\u5916\u7684IP\u5730\u5740\u3002\n\n-p | --port\n    \u8bbe\u7f6e\u4f7f\u7528\u7684\u7aef\u53e3\u53f7\uff0c\u9ed8\u8ba4\u4e3a4567\u3002<\/pre>\n\n\n\n
3.2 \u63d0\u4f9b\u7a33\u5b9a\u7684\u7f51\u7ad9\u670d\u52a1<\/h2>\n\n\n\n
\u5148\u51c6\u5907\u7a0b\u5e8f\u7684\u914d\u7f6e\u6587\u4ef6\/etc\/sequenceserver.conf\uff0c\u7528\u4e8e\u8bbe\u7f6e\u7a0b\u5e8f\u8fd0\u884c\u53c2\u6570\u548c\u8f93\u5165\u6570\u636e\u3002\u5176\u5185\u5bb9\u793a\u4f8b\u5982\u4e0b\uff0c\u6839\u636e\u5b9e\u9645\u60c5\u51b5\u4fee\u6539host\u4e3a\u5bf9\u5916\u7684IP\u5730\u5740\uff0c\u4fee\u6539NCBI-Blast+\u7684bin\u76ee\u5f55\u8def\u5f84\u548c\u6570\u636e\u5e93\u6587\u4ef6\u5939\u8def\u5f84\uff0c\u4fee\u6539\u9632\u706b\u5899\u7aef\u53e3\u5f00\u653e\u8bbe\u7f6e\u3002<\/p>\n\n\n\n
---\n:host: 10.0.0.5\n:port: 4567\n:databases_widget: tree\n:options:\n  :blastn:\n    :default:\n    - \"-task blastn\"\n    - \"-evalue 1e-5\"\n    :custom:\n    - \"-task blastn\"\n    - \"-evalue 1e-5 -num_alignments 20\"\n  :blastp:\n    :default:\n    - \"-evalue 1e-5\"\n    :custom:\n    - \"-evalue 1e-5 -num_alignments 20\"\n  :blastx:\n    :default:\n    - \"-evalue 1e-5\"\n    :custom:\n    - \"-evalue 1e-5 -num_alignments 20\"\n  :tblastx:\n    :default:\n    - \"-evalue 1e-5\"\n    :custom:\n    - \"-evalue 1e-5 -num_alignments 20\"\n  :tblastn:\n    :default:\n    - \"-evalue 1e-5\"\n    :custom:\n    - \"-evalue 1e-5 -num_alignments 20\"\n:num_threads: 32\n:num_jobs: 4\n:job_lifetime: 43200\n:cloud_share_url: https:\/\/share.sequenceserver.com\/api\/v1\/shared-job\n\n:bin: \"\/opt\/biosoft\/ncbi-blast-2.14.0+\/bin\"\n:database_dir: \"\/disks\/xxx\/NCBI_blast_databases\"<\/pre>\n\n\n\n
\u7136\u540e\uff0c\u751f\u6210\u6587\u4ef6\/etc\/systemd\/system\/sequenceserver.service\uff0c\u7528\u4e8e\u4f5c\u5f00\u673a\u542f\u52a8\u3002\u5176\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n\n\n\n
[Unit]\r\nDescription=SequenceServer server daemon\r\nDocumentation=\"file:\/\/sequenceserver --help\" \"http:\/\/sequenceserver.com\/doc\"\r\nAfter=network.target\r\n\r\n[Service]\r\nType=simple\r\nUser=root\r\nExecStart=\/opt\/sysoft\/ruby-3.1.2\/bin\/sequenceserver -c \/etc\/sequenceserver.conf\r\nKillMode=process\r\nRestart=on-failure\r\nRestartSec=42s\r\nRestartPreventExitStatus=255\r\n\r\n[Install]\r\nWantedBy=multi-user.target<\/pre>\n\n\n\n
\u8ba9\u5f00\u673a\u542f\u52a8\u914d\u7f6e\u6587\u4ef6\u751f\u6548\uff0c\u5e76\u542f\u52a8\u670d\u52a1\u3002<\/p>\n\n\n\n
sudo systemctl restart sequenceserver.service\r\nsudo systemctl enable sequenceserver.service<\/code><\/pre>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
1. \u7b80\u4ecb \u73b0\u5728NCBI\u4e0d\u518d\u63d0\u4f9bwwwblast\u8f6f\u4ef6\u4e0b\u8f7d\u3002\u4e14NCBI\u7684wwwbl … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2673"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2673"}],"version-history":[{"count":6,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2673\/revisions"}],"predecessor-version":[{"id":3783,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2673\/revisions\/3783"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2673"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2673"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2673"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}