{"id":228,"date":"2012-09-01T11:21:30","date_gmt":"2012-09-01T03:21:30","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=228"},"modified":"2012-11-20T17:27:45","modified_gmt":"2012-11-20T09:27:45","slug":"sequenceserver%e7%9a%84%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=228","title":{"rendered":"SequenceServer\u7684\u5b89\u88c5"},"content":{"rendered":"<p>\u51fa\u81eahttp:\/\/www.sequenceserver.com\/<\/p>\n<p>SequenceServer\u8fd9\u4e2a\u8f6f\u4ef6\u5f00\u53d1\u51fa\u6765\u4e0d\u4e45\u3002\u5176\u4f5c\u7528\u662f\u5c06 blast+ \u6574\u5408\u5230\u672c\u5730\u7f51\u7edc\u4e2d\u3002\u80fd\u81ea\u52a8\u8bc6\u522b\u51fa\u672c\u5730\u7684\u6570\u636e\u5e93\uff0c\u754c\u9762\u7b80\u6d01\u6613\u7528\u3002\u548c wwwblast \u529f\u80fd\u7c7b\u4f3c\u3002<\/p>\n<h1>1 \u5b89\u88c5\u9700\u8981<a href=\"http:\/\/ruby-lang.org\/\">Ruby<\/a> (&gt;= 1.8.7), <a href=\"https:\/\/rubygems.org\/\">RubyGems<\/a> (&gt;= 1.3.6), and <a href=\"ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.2.25\/\">NCBI BLAST+<\/a> (&gt;= 2.2.25+).<\/h1>\n<pre># yum install *ruby*  #\u5b89\u88c5\u5f88\u591aruby\u76f8\u5173\u8f6f\u4ef6\uff0c\u4e0d\u7136\u8fd0\u884c\u4f1a\u51fa\u95ee\u9898\uff0c\u7279\u522b\u662f\u7f3a\u5c11\r\nruby-devel\r\nNCBI BLAST+ ftp:\/\/ftp.ncbi.nih.gov\/blast\/executables\/blast+\/LATEST\/<\/pre>\n<h1>2 \u5b89\u88c5sequenceserver<\/h1>\n<pre># gem install sequenceserver<\/pre>\n<h1>3\u00a0 \u914d\u7f6esequenceserver<\/h1>\n<pre># <code><\/code>sequenceserver\u00a0\u00a0 \u8fd0\u884c\u8f6f\u4ef6\u751f\u6210\u5e26\u6709\u6ce8\u91ca\u7684\u914d\u7f6e\u6587\u4ef6\r\n# vim <code>.sequenceserver.conf<\/code> \u5c06\u6ce8\u91ca\u6587\u4ef6\u8fdb\u884c\u4fee\u6539\uff0c\u52a0\u5165blast\u8def\u5f84\r\nbin: ~\/ncbi-blast-2.2.26+\/bin\/\r\ndatabase: \/Users\/me\/blast_databases\/<\/pre>\n<h1>4 blast\u6570\u636e\u5e93\u7684\u521b\u5efa<\/h1>\n<p>&lt;1&gt; \u4f7f\u7528 sequenceserver \u6765\u8c03\u7528 makeblastdb \u8fdb\u884c\u6570\u636e\u5e93\u521b\u5efa<\/p>\n<pre>$ sequenceserver format-databases directory_with_fasta_files<\/pre>\n<p>&lt;2&gt; \u4f7f\u7528 blast+ \u672c\u8eab\u6240\u5e26 makeblastdb \u6765\u521b\u5efa\u6570\u636e\u5e93<\/p>\n<pre>$ makeblastdb -dbtype &lt;db type&gt; -title &lt;db title&gt; -in &lt;db&gt; -parse_seqids<\/pre>\n<h1>5 \u901a\u8fc7 passenger \u5728 Apache \u6216 Nginx \u4e0a\u8fd0\u884c SequenceServer<\/h1>\n<pre># gem install passenger\r\n\r\nfor apache2 \r\n# passenger-install-apache2-module \u00a0 #\u6309\u63d0\u793a\u8fdb\u884c\u8bbe\u7f6e\r\n\r\nfor nginx \r\n# passenger-install-nginx-module<\/pre>\n<h1>6 \u90e8\u7f72\u670d\u52a1\u5668\u8bbe\u7f6e<\/h1>\n<pre>\u5728 https:\/\/github.com\/yannickwurm\/sequenceserver \u4e0b\u8f7d sequencesercer \r\n\u5c06 sequenceserver-0.8.0.3.zip \u89e3\u538b\u5230 \/var\/www\/sequenceserver\/. \u4f7f\u8be5\u6587\r\n\u4ef6\u5939\u4e0b\u5b58\u5728 public \u8fd9\u4e2a\u6587\u4ef6\u5939\u3002<\/pre>\n<pre># vim \/etc\/http\/conf\/http.conf \u00a0\u5e76\u52a0\u5165\u4ee5\u4e0b\u6570\u884c\r\n\r\n&lt;VirtualHost *:80&gt;\r\n\u00a0\u00a0\u00a0 DocumentRoot \/var\/www\/sequenceserver\/public\r\n\u00a0\u00a0\u00a0 ServerName http:\/\/sequenceserver.hzaumycology.com\r\n#\u524d\u63d0\u6761\u4ef6\u662f\u7533\u8bf7\u4e86sequenceserver.hzaumycology.com\u8fd9\u4e2a\u57df\u540d\r\n\u00a0\u00a0\u00a0 &lt;Directory \/var\/www\/sequenceserver\/public&gt;\r\n\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 AllowOverride all\r\n\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Options -MultiViews\r\n\u00a0\u00a0\u00a0 &lt;\/Directory&gt;\r\n&lt;\/VirtualHost&gt;\r\n\r\n# \/etc\/init.d\/httpd restart<\/pre>\n<h1>7 \u8fd0\u884c<code> passenger<\/code> \u548c sequenceserver<\/h1>\n<pre># nohup <code>passenger<\/code> start &amp;\r\n# nohup sequenceserver &amp;\r\n\r\n\u82e5\u60f3\u8981\u5f00\u673a\u8fd0\u884c\u8fd9\u4e24\u4e2a\u547d\u4ee4\uff0c\u5219\r\n# vim \/etc\/rc.local \u00a0\u5728\u672b\u5c3e\u6dfb\u52a0<code> passenger<\/code> start &amp;\r\nsequenceserver &amp;<\/pre>\n<h1>\u00a08 \u4fee\u6539 .sequenceserver.conf \u914d\u7f6e\u6587\u4ef6<\/h1>\n<pre>\u53ef\u4ee5\u9009\u62e9\u4fee\u6539\u7aef\u53e3\uff0c\u9ed8\u8ba4\u7aef\u53e3\u4e3a4567\uff0c\u5219\u8981\r\n# vim \/etc\/sysconfig\/iptables \u00a0 \u5728\u76f8\u5e94\u4f4d\u7f6e\u52a0\u5165\u4e00\u884c\r\n-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4567 -j ACCEPT\r\n# \/etc\/init.d\/iptables restart \u00a0 \u91cd\u542fiptables\u670d\u52a1\r\n\r\n\u6839\u636e\u670d\u52a1\u5668\u914d\u7f6e\u4fee\u6539\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u4e3a1.<\/pre>\n<h1>9\u00a0 \u4ee5\u4e0a\u914d\u7f6e\u4e0d\u51fa\u73b0\u9519\u8bef\uff0c\u5219\u53ef\u4ee5\u5728\u6d4f\u89c8\u5668\u4e2d\u8fdb\u884c sequenceserver \u8bbf\u95ee\u4e86.<\/h1>\n<pre>\u6d4f\u89c8\u5668\u4e2d\u8f93\u5165\uff1a http:\/\/sequenceserver.hzaumycology.com:4567<\/pre>\n<p>\u5219\u4f1a\u51fa\u73b0\u4e00\u4e2a\u7b80\u6d01\u6f02\u4eae\u7684\u754c\u9762\u4e86\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u51fa\u81eahttp:\/\/www.sequenceserver.com\/ Sequenc &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=228\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[8],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/228"}],"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=228"}],"version-history":[{"count":10,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/228\/revisions"}],"predecessor-version":[{"id":230,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/228\/revisions\/230"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=228"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=228"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=228"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}