{"id":2296,"date":"2015-08-25T16:42:38","date_gmt":"2015-08-25T08:42:38","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2296"},"modified":"2015-08-25T16:42:38","modified_gmt":"2015-08-25T08:42:38","slug":"web-apollo-%e7%9a%84%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2296","title":{"rendered":"Web Apollo \u7684\u5b89\u88c5"},"content":{"rendered":"<h1>1. \u7b80\u4ecb<\/h1>\n<p><a href=\"http:\/\/webapollo.readthedocs.org\" target=\"_blank\">Web Apollo<\/a> \u5c5e\u4e8e JBrowse \u7684\u4e00\u4e2a\u63d2\u4ef6\uff0c\u53ef\u7528\u4e8e\u57fa\u56e0\u7ec4\u6ce8\u91ca\u7684\u624b\u5de5\u4fee\u6b63\u3002\u7531\u4e8e\u901a\u8fc7\u5728\u7f51\u9875\u4e0a\u8fdb\u884c\u624b\u5de5\u4fee\u6b63\uff0c\u53ef\u4ee5\u7531\u591a\u4e2a\u4e0d\u540c\u5730\u7406\u4f4d\u7f6e\u7684\u4eba\u5458\u8fdb\u884c\u4fee\u6b63\u3002<br \/>\nWeb Apollo \u6bd4\u8f83\u96be\u4ee5\u5b89\u88c5\uff0c\u65b0\u7248\u5b89\u88c5\u8bf4\u660e\uff1a <a href=\"http:\/\/webapollo.readthedocs.org\/en\/latest\/\" target=\"_blank\">http:\/\/webapollo.readthedocs.org\/en\/latest\/<\/a>\uff1b 2014-04-03 \u7248\u672c\u7684\u5b89\u88c5\u8bf4\u660e\uff1a <a href=\"http:\/\/www.gmod.org\/wiki\/WebApollo_Installation\" target=\"_blank\">http:\/\/www.gmod.org\/wiki\/WebApollo_Installation<\/a>\u3002\u63a8\u8350\u53c2\u8003\u540e\u8005\u3002<\/p>\n<h1>2. Web Apollo \u7684\u5b89\u88c5\u6b65\u9aa4<\/h1>\n<h2>2.1 \u5b89\u88c5 Perl \u6a21\u5757\uff0cPostGreSQL \u6570\u636e\u5e93<\/h2>\n<p>\u5b89\u88c5 Web Apollo \u4e4b\u524d\uff0c\u9700\u8981\u5b89\u88c5\u4e00\u4e9b perl \u6a21\u5757\u3001 PostGreSQL \u6570\u636e\u5e93\u548c Tomcat 7\u3002<\/p>\n<pre>\u5b89\u88c5 Perl \u6a21\u5757\u6bd4\u8f83\u9ebb\u70e6\u8017\u65f6\uff0c\u6709\u4e9b Perl \u6a21\u5757\u4e0d\u5bb9\u6613\u5b89\u88c5\u4e0a\u53bb\uff0c\u9700\u8981\u8010\u5fc3\u3002\u5728\u5176\u5b83\u5b89\u88c5\u8fc7\u7a0b\u4e2d\uff0c\u53ef\u80fd\u63d0\u793a\u7f3a\u5c11\u4e00\u4e9b Perl \u6a21\u5757\uff0c\u5b89\u88c5\u76f8\u5e94\u7684 Perl \u6a21\u5757\u5373\u53ef\r\n$ sudo cpan -i BioPerl JSON JSON::XS PerlIO::gzip Heap::Simple Heap::Simple::XS Devel::Size Hash::Merge Bio::GFF3::LowLevel::Parser  Digest::Crc32  Cache::Ref::FIFO\r\n\r\n\u5b89\u88c5 PostGreSQL\r\n$ sudo yum install postgresql postgresql-devel\r\n\r\n\u542f\u52a8 PostGreSQL\uff0c \u7b2c\u4e00\u6b21\u542f\u52a8\u5219\u4f1a\u751f\u6210\u521d\u59cb\u5316\u7684\u6587\u4ef6\u3002\r\n$ sudo \/etc\/init.d\/postgresql start\r\n\r\n\u4fee\u6539 PostGreSQL \u914d\u7f6e\u6587\u4ef6  \/var\/lib\/pgsql\/data\/pg_hba.conf\uff0c\u5728\u5c3e\u90e8\u52a0\u5165\u4e00\u884c\u5185\u5bb9\uff0c\u8868\u793a\u7528\u6237 chenlianfu \u901a\u8fc7\u5bc6\u7801\u8fde\u63a5 postgres \u6570\u636e\u5e93\u3002\r\n$ sudo echo \"local   all         chenlianfu                        md5\" &gt;&gt; \/var\/lib\/pgsql\/data\/pg_hba.conf<\/pre>\n<h2>2.2 \u4e0b\u8f7d\u5e76\u89e3\u538b\u7f29 Web Apollo \u548c Tomcat 7<\/h2>\n<p>\u63a8\u8350\u4f7f\u7528 2014-04-03 \u7248\u672c\u7684 Web Apollo\u3002<br \/>\n\u4f7f\u7528 CentOS yum \u5b89\u88c5\u7684 Tomcat 7 \u8c8c\u4f3c\u4e0d\u53ef\u7528\uff0c\u56e0\u6b64\u63a8\u8350\u76f4\u63a5\u4e0b\u8f7d\u4e8c\u8fdb\u5236\u7248\u672c\u7684 Tomcat 7\u3002<\/p>\n<pre>\u4e0b\u8f7d\u5e76\u89e3\u538b\u7f29 Web Apollo 2014-04-03\r\n$ wget http:\/\/icebox.lbl.gov\/webapollo\/releases\/previous_releases\/WebApollo-2014-04-03.tgz\r\n$ tar zxf WebApollo-2014-04-03.tgz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/WebApollo-2014-04-03\r\n\r\n\u4e0b\u8f7d\u5e76\u89e3\u538b\u7f29\u793a\u4f8b\u6570\u636e\r\n$ wget http:\/\/icebox.lbl.gov\/webapollo\/data\/pyu_data.tgz\r\n$ tar zxf pyu_data.tgz\r\n\r\n\u4e0b\u8f7d Tomcat 7 \u7684\u4e8c\u8fdb\u5236\u7248\u672c\r\n$ wget http:\/\/apache.fayea.com\/tomcat\/tomcat-7\/v7.0.57\/bin\/apache-tomcat-7.0.57.tar.gz\r\n$ tar zxf apache-tomcat-7.0.57.tar.gz\r\n\r\n\u4fee\u6539 Tomcat 7 \u914d\u7f6e\u6587\u4ef6\r\n$ cd apache-tomcat-7.0.57\r\n\u4fee\u6539 Tomcat 7 \u7684\u62a5\u9519\u8bbe\u7f6e\r\n$ perl -p -i -e 's\/(autoDeploy=.*)&gt;\/$1\\n            errorReportValveClass=\"org.bbop.apollo.web.ErrorReportValve\"&gt;\/' conf\/server.xml\r\n\u4fee\u6539 Tomcat 7 \u7684\u5185\u5b58\u8bbe\u7f6e\uff0c\u63a8\u8350\u8bbe\u7f6e heap size \u81f3\u5c11 1G\uff0c permgen size \u81f3\u5c11 256M\uff0c\u57fa\u56e0\u7ec4\u8d8a\u5927\uff0c\u8bbe\u7f6e\u8d8a\u5927\u3002\r\n$ perl -p -i -e 's\/cygwin=false\/CATALINA_OPTS=\"-Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m\"\\ncygwin=false\/' bin\/catalina.sh<\/pre>\n<h2>2.3 \u90e8\u7f72 Web Apollo<\/h2>\n<pre>$ cd apache-tomcat-7.0.57\/webapps\/\r\n$ mkdir webApollo_Pythium_ultimum\r\n$ cd webApollo_Pythium_ultimum\r\n$ jar -xvf \/opt\/biosoft\/WebApollo-2014-04-03\/war\/WebApollo.war\r\n$ chmod 755 jbrowse\/bin\/*\r\n\r\n\u5c06 JBrowse \u6570\u636e\u6587\u4ef6\u5939\u94fe\u63a5\u8fc7\u6765\r\n$ ln -s \/opt\/biosoft\/WebApollo-2014-04-03\/data_Pythium_ultimum data<\/pre>\n<p>\u5176\u5b9e\uff0c\u5230\u8fd9\u4e00\u6b65\uff0cWeb Apollo \u7b97\u662f\u5b89\u88c5\u5b8c\u6bd5\u4e86\uff0c\u53ea\u9700\u8981\u901a\u8fc7 tomcat \u8bbf\u95ee\u5176 webapps \u6587\u4ef6\u5939\u4e0b\u7684\u5185\u5bb9\u5373\u53ef\u3002\u4f46\u662f\u73b0\u5728\u8bbf\u95ee\u662f\u6ca1\u7528\u7684\uff0c\u8fd8\u9700\u8981\u8bbe\u7f6e\u4e00\u4e9b\u914d\u7f6e\u6587\u4ef6\uff0c\u544a\u8bc9 tomcat \u4f7f\u7528\u76f8\u5e94\u7684\u7528\u6237\u6765\u8bbf\u95ee PostGres \u6570\u636e\u5e93\u5185\u5bb9\u548c JBrowse \u6570\u636e\u6587\u4ef6\u3002\u800c\u8fd9\u4e9b\u7528\u6237\u4e0e\u6743\u9650\u8bbe\u7f6e\uff0c\u4ee5\u53ca JBrowse \u6570\u636e\u6587\u4ef6\u5efa\u7acb\u662f\u96be\u70b9\u3002\u5728\u5982\u4e0a\u4e24\u70b9\u51c6\u5907\u5b8c\u6bd5\u540e\uff0c\u5373\u53ef\u4fee\u6539 webapp \u7684\u914d\u7f6e\u6587\u4ef6\u6765\u8fde\u901a\u76f8\u5e94\u7684\u6570\u636e\u4fe1\u606f\uff0c\u4ece\u800c\u5f97\u5230\u7f51\u9875\u5c55\u793a\u7ed3\u679c\u3002<\/p>\n<h2>2.4 \u8bbe\u7f6e PostGres \u548c Web Apollo \u7684\u7528\u6237\uff0c\u6570\u636e\u5e93\u548c\u6743\u9650<\/h2>\n<p>Web Apollo \u7f51\u9875\u4e2d\u7684\u7528\u6237\u540d\u548c\u5bc6\u7801\uff0c\u4ee5\u53ca\u7528\u6237\u5bf9\u67d0\u6761\u5e8f\u5217\u7684\u4fee\u6539\u6743\u9650\u5b58\u50a8\u4e8e PostGres \u6570\u636e\u5e93\u4e2d\uff0c\u56e0\u6b64\u9700\u8981\u5efa\u7acb PostGres \u7684\u7528\u6237\u548c\u6570\u636e\u5e93\u3002<\/p>\n<pre>\u521b\u5efa postgres \u7528\u6237 chenlianfu \uff0c\u5bc6\u7801 123456\u3002 \u548c\u4e0a\u9762\u914d\u7f6e\u6587\u4ef6\u76f8\u5bf9\u5e94\u3002\u8be5\u7528\u6237\u5fc5\u987b\u662f Linux \u7cfb\u7edf\u7528\u6237\r\n$ sudo su  postgres\r\n$ createuser -P chenlianfu\r\nEnter password for new role: \r\nEnter it again: \r\nShall the new role be a superuser? (y\/n) n\r\nShall the new role be allowed to create databases? (y\/n) y\r\nShall the new role be allowed to create more new roles? (y\/n) n\r\n\r\n\u521b\u5efa PostGres \u6570\u636e\u5e93\r\n$ createdb -U chenlianfu apollo_Pythium_ultimum\r\n\r\n\u5efa\u7acb\u6570\u636e\u5e93\u7684\u8868\r\n$ cd \/opt\/biosoft\/WebApollo-2014-04-03\/\r\n$ cd tools\/user\/\r\n$ psql -U chenlianfu apollo_Pythium_ultimum &lt; user_database_postgresql.sql\r\n\r\n\u521b\u5efa Web Apollo \u7528\u6237 apollo\uff0c\u5bc6\u7801 123456\r\n.\/add_user.pl -D apollo_Pythium_ultimum -U chenlianfu -P 123456 -u apollo -p 123456\r\n\r\n\u63d0\u53d6\u57fa\u56e0\u7ec4\u5e8f\u5217\u540d\uff0c\u5c06\u5e8f\u5217\u540d\u5bfc\u5165\u5230 postgres \u6570\u636e\u5e93\uff0c\u5e76\u4f7f apollo \u7528\u6237\u5177\u6709\u8bbf\u95ee\u8fd9\u4e9b\u5e8f\u5217\u7684\u6743\u9650\r\n$ cd ..\/..\/\r\n$ .\/tools\/user\/extract_seqids_from_fasta.pl -p Annotations- -i pyu_data\/scf1117875582023.fa -o seqids.txt\r\n$ .\/tools\/user\/add_tracks.pl -D apollo_Pythium_ultimum -U chenlianfu -P 123456 -t seqids.txt\r\n$ .\/tools\/user\/set_track_permissions.pl -D apollo_Pythium_ultimum -U chenlianfu -P 123456 -u apollo -t seqids.txt -a<\/pre>\n<h2>2.5 Jbrowse \u6570\u636e\u6587\u4ef6\u5236\u4f5c<\/h2>\n<pre>$ cd \/opt\/biosoft\/WebApollo-2014-04-03\/\r\n\r\n\u521b\u5efa 2 \u4e2a\u6587\u4ef6\u5939\uff0c\u524d\u8005\u7528\u4e8e\u5b58\u653e Web Apollo \u4fee\u6539\u7684\u6570\u636e\u4e0e\u5386\u53f2\u75d5\u8ff9\uff0c\u540e\u8005\u7528\u4e8e\u5b58\u653e JBrowse \u7684\u6570\u636e\r\n$ mkdir annotations_Pythium_ultimum data_Pythium_ultimum\r\n\r\n\u5bf9 fasta \u6587\u4ef6\u8fdb\u884c JBrowse Track \u8bbe\u7f6e\r\n$ .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/prepare-refseqs.pl \\\r\n    --fasta pyu_data\/scf1117875582023.fa\r\n\u6dfb\u52a0 webApollo \u63d2\u4ef6\r\n$ .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/add-webapollo-plugin.pl \\\r\n    -i data\/trackList.json\r\n\r\n\u5148\u5c06\u793a\u4f8b\u6587\u4ef6\u4e2d\u7684 maker output \u8fdb\u884c\u5206\u5272\uff0c\u6210\u4e3a\u4e0d\u540c source \u7684 GFF3 \u6587\u4ef6\r\n$ mkdir pyu_data\/split_gff\r\n$ .\/tools\/data\/split_gff_by_source.pl -i pyu_data\/scf1117875582023.gff -d pyu_data\/split_gff\/\r\n\r\n\u5bf9 GFF3 \u6587\u4ef6\u8fdb\u884c JBrowse Track \u8bbe\u7f6e\r\n$ .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/flatfile-to-json.pl \\\r\n    --gff pyu_data\/split_gff\/maker.gff --arrowheadClass trellis-arrowhead --getSubfeatures \\\r\n    --subfeatureClasses '{\"wholeCDS\": null, \"CDS\":\"brightgreen-80pct\", \"UTR\": \"darkgreen-60pct\", \"exon\":\"container-100pct\"}' \\\r\n    --className container-16px --type mRNA --trackLabel maker\r\n$ for i in `ls pyu_data\/split_gff\/ | grep -v maker`\r\ndo\r\n    i=${i##*\/}\r\n    i=${i\/.gff\/}\r\n    .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/flatfile-to-json.pl \\\r\n    --gff pyu_data\/split_gff\/$i.gff --arrowheadClass webapollo-arrowhead --getSubfeatures \\\r\n    --subfeatureClasses '{\"match_part\": \"darkblue-80pct\"}' --className container-10px --trackLabel $i\r\ndone\r\n\r\nJBrowse Track \u5efa\u7acb\u5b8c\u6bd5\uff0c\u518d\u521b\u5efa\u7d22\u5f15\r\n$ .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/generate-names.pl\r\n\r\nBAM \u6570\u636e\u8bbe\u7f6e\r\n$ mkdir data\/bam\r\n$ cp pyu_data\/*.bam* data\/bam\/\r\n$ .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/add-bam-track.pl \\\r\n    --bam_url bam\/simulated-sorted.bam --label simulated_bam --key \"simulated BAM\"\r\n\r\nBigWig \u6570\u636e\u8bbe\u7f6e\r\n$ mkdir data\/bigwig\r\n$ cp pyu_data\/*.bw data\/bigwig\/\r\n$ .\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/bin\/add-bw-track.pl \\\r\n    --bw_url bigwig\/simulated-sorted.coverage.bw --label simulated_bw --key \"simulated BigWig\"\r\n\r\nrm data_Pythium_ultimu\r\nmv data data_Pythium_ultimu<\/pre>\n<h2>2.6 Web Apollo \u914d\u7f6e<\/h2>\n<p>\u914d\u7f6e Web Apollo \u5728 tomcat \u4e2d\u7684 webapp \u8bbe\u7f6e\uff0c\u4ece\u800c\u5c55\u793a JBrowse \u6570\u636e\u3002\u540c\u65f6\uff0c\u8fde\u63a5 PostGres \u6570\u636e\u5e93\u4ece\u800c\u8bbe\u7f6e\u5f97\u5230 Web Apollo \u7528\u6237\u548c\u6743\u9650\u4fe1\u606f\u3002<br \/>\n\u914d\u7f6e\u6587\u4ef6\u5b58\u653e\u8def\u5f84\uff1a \/opt\/biosoft\/WebApollo-2014-04-03\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/config<\/p>\n<p>\u4e3b\u8981\u914d\u7f6e\u6587\u4ef6\u662f config.xml\uff0c\u4fee\u6539\u5185\u5bb9\uff1a<\/p>\n<pre>\u8bbe\u7f6e Web Apollo \u7684\u4fee\u6539\u7ed3\u679c\u5b58\u653e\u8def\u5f84\r\n&lt;datastore_directory&gt;\/opt\/biosoft\/WebApollo-2014-04-03\/annotations_Pythium_ultimum\/&lt;\/datastore_directory&gt;\r\n\r\n\u8bbe\u7f6e intron \u6700\u5c0f\u957f\u5ea6\r\n&lt;default_minimum_intron_size&gt;40&lt;\/default_minimum_intron_size&gt;\r\n\r\n\u8bbe\u7f6e PostGres \u6570\u636e\u5e93\u767b\u5f55\u53c2\u6570\r\n&lt;database&gt;\r\n    &lt;driver&gt;org.postgresql.Driver&lt;\/driver&gt;\r\n    &lt;url&gt;jdbc:postgresql:\/\/localhost\/apollo_Pythium_ultimum&lt;\/url&gt;\r\n    &lt;username&gt;chenlianfu&lt;\/username&gt;\r\n    &lt;password&gt;123456&lt;\/password&gt;\r\n&lt;\/database&gt;\r\n\r\n\u8bbe\u7f6e JBrowse \u7684 refSeqs.json \u6587\u4ef6\u8def\u5f84\r\n&lt;refseqs&gt;\/opt\/biosoft\/WebApollo-2014-04-03\/apache-tomcat-7.0.57\/webapps\/webApollo_Pythium_ultimum\/jbrowse\/data\/seq\/refSeqs.json&lt;\/refseqs&gt;\r\n\r\n\u8bbe\u7f6e\u7269\u79cd\u540d\uff0c\u5fc5\u987b\u4e3a 2 \u4e2a\u5355\u8bcd\r\n&lt;organism&gt;Pythium ultimum&lt;\/organism&gt;\r\n\r\n\u8bbe\u7f6e\u57fa\u56e0\u7ec4\u5e8f\u5217\u7c7b\u578b\r\n&lt;sequence_type&gt;sequence:scaffold&lt;\/sequence_type&gt;\r\n\r\n\u8bbe\u7f6e\u81ea\u5b9a\u4e49\u7684 feature_type, \u53bb\u6389\u8be5\u6bb5\u6ce8\u91ca\uff0c\u4f7f\u4e4b\u751f\u6548\r\n&lt;status&gt;\r\n    &lt;status_flag&gt;Approved&lt;\/status_flag&gt;\r\n    &lt;status_flag&gt;Needs review&lt;\/status_flag&gt;\r\n&lt;\/status&gt;\r\n\r\n\u8bbe\u7f6e GFF3 \u6587\u4ef6\u7684 data_adapter\r\n&lt;data_adapter&gt;\r\n    &lt;key&gt;GFF3&lt;\/key&gt;\r\n    &lt;class&gt;org.bbop.apollo.web.dataadapter.gff3.Gff3DataAdapter&lt;\/class&gt;\r\n    &lt;permission&gt;publish&lt;\/permission&gt;\r\n    &lt;config&gt;\/config\/gff3_config.xml&lt;\/config&gt;\r\n    &lt;options&gt;output=file&amp;amp;format=gzip&lt;\/options&gt;\r\n&lt;\/data_adapter&gt;<\/pre>\n<p>\u5728\u4e3b\u914d\u7f6e\u6587\u4ef6\u4e2d\uff0c\u5305\u542b\u4e86\u5176\u5b83\u914d\u7f6e\u6587\u4ef6\u7684\u8def\u5f84\u3002\u5bf9 blat_config.xml \u8fdb\u884c\u4fee\u6539\uff0c\u662f Web Apollo \u7684 blat \u5de5\u5177\u751f\u6548\u3002\u9700\u8981 blat \u547d\u4ee4\u548c\u6570\u636e\u5e93\u6587\u4ef6\u3002<br \/>\n\u4f7f\u7528 blat \u8f6f\u4ef6\u4e2d\u7684 faToTwoBit \u547d\u4ee4\u751f\u6210 blat \u7684\u6570\u636e\u5e93\u6587\u4ef6<\/p>\n<pre>$ cd \/opt\/biosoft\/WebApollo-2014-04-03\r\n$ faToTwoBit pyu_data\/scf1117875582023.fa pyu_data\/scf1117875582023.2bi\r\nt<\/pre>\n<p>\u4fee\u6539 blat_config.xml \u7684\u6587\u4ef6\u5185\u5bb9<\/p>\n<pre>\u8bbe\u7f6e blat \u547d\u4ee4\u8def\u5f84\r\n&lt;blat_bin&gt;\/opt\/biosoft\/blat\/bin\/blat&lt;\/blat_bin&gt;\r\n\r\n\u8bbe\u7f6e blat \u7684\u8f93\u51fa\u6587\u4ef6\u8def\u5f84\r\n&lt;tmp_dir&gt;\/opt\/biosoft\/WebApollo-2014-04-03\/pyu_data\/&lt;\/tmp_dir&gt;\r\n\r\n\u8bbe\u7f6e\u6570\u636e\u5e93\u6587\u4ef6\r\n&lt;database&gt;\/opt\/biosoft\/WebApollo-2014-04-03\/pyu_data\/scf1117875582023.2bit&lt;\/database&gt;\r\n\r\n\u8bbe\u7f6e blat \u53c2\u6570\r\n&lt;blat_options&gt;-minScore=100 -minIdentity=60&lt;\/blat_options&gt;<\/pre>\n<p>\u5176\u5b83\u914d\u7f6e\u6587\u4ef6 canned_comments.xml\uff0c gff3_config.xml\uff0c hibernate.xml\uff0c chado_config.xml \u7b49\u4e5f\u8981\u7ecf\u8fc7\u4e00\u4e9b\u4fee\u6539\u3002<\/p>\n<h2>2.7 \u8fd0\u884c Web Apollo<\/h2>\n<pre>$ cd \/opt\/biosoft\/WebApollo-2014-04-03\r\n$ .\/apache-tomcat-7.0.57\/bin\/startup.sh<\/pre>\n<p>\u5f00\u542f tomcat \u670d\u52a1\u540e\uff0c\u5373\u53ef\u8bbf\u95ee web Apollo \u4e86\u3002 \u7531\u4e8e\u5c06 web Apollo \u5b89\u88c5\u5728\u4e86\u670d\u52a1\u5668\u4e0a\uff0c\u8bbf\u95ee\u670d\u52a1\u5668 IP 8080\u7aef\u53e3\uff1a www.chenlianfu.com:8080\/<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. \u7b80\u4ecb Web Apollo \u5c5e\u4e8e JBrowse \u7684\u4e00\u4e2a\u63d2\u4ef6\uff0c\u53ef\u7528\u4e8e\u57fa\u56e0\u7ec4 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2296\">\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":[72],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2296"}],"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=2296"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2296\/revisions"}],"predecessor-version":[{"id":2297,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2296\/revisions\/2297"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2296"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2296"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2296"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}