UCSC基因組瀏覽器在大規模高通量數據的可視化和比較分析研究中發揮著重要的作用。擁有了本地瀏覽器，就可以對自己的測序數據進行更深入的分析和共享使用。本文詳細介紹了如何一步步在本地安裝、配置、高級使用UCSC瀏覽器。

安裝UCSC瀏覽器

1. 安裝mysql+apache

#For Ubuntu usersudo apt-get install taskselsudo apt-get install lamp-server#For readhat or centos user yum install httpd mariadb-server mariadb

2. 新建mysql用戶

# 用戶名：gw # 密碼 ?：qazplm_gw create user 'gw'@'localhost' identified by 'qazplm_gw';

3. 同步UCSC所需html文件和運行程序

# 設置UCSC的安裝目錄為 /var/www/gw mkdir /var/www/gw# 同步相應的html文件 rsync -avzP --exclude 'ENCODE' rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/gw# 同步可執行程序到cgi-bin目錄下mkdir /var/www/gw/cgi-bin# For 64-bit rsync -avzP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ /var/www/gw/cgi-bin/ ?#64 bit# 更改cgi-bin目錄的所有者 chown -R www-data.www-data /var/www/gw/cgi-bin/

4. 把以下內容寫入/etc/apahce2/httpd.conf

# XBitHack on 是必須的 # 其它參數的意思參見apache文檔 XBitHack on <Directory /var/www/gw> ? AllowOverride AuthConfigOptions +Includes </Directory># the ScriptAlias directive is crucialScriptAlias /gw/cgi-bin /var/www/gw/cgi-bin <Directory "/var/www/gw/cgi-bin">AllowOverride NoneOptions +ExecCGI -MultiViews +SymLinksIfOwnerMatchOrder allow,denyAllow from allAddHandler cgi-script cgi pl</Directory>

5. 設置Apache解析有執行權限的文件中的SSI指令，然后重啟apache

ln -s /etc/apache2/mods-available/include.load /etc/apache2/mods-enabled//etc/init.d/apache2 restart

6. 設置數據庫配置文件

進入/var/www/gw/cgi-bin/目錄，建立hg.conf文件并寫入下列內容

db.host=localhost db.user=gw db.password=qazplm_gw db.trackDb=trackDbcentral.db=hgcentral central.host=localhost central.user=gw central.password=qazplm_gw central.domain=backupcentral.db=hgcentral backupcentral.host=localhost backupcentral.user=gw backupcentral.password=qazplm_gw backupcentral.domain=

同時運行如下命令sudo chown www-data /var/www/gw/cgi-bin/hg.conf更改文件的所有權。

更多功能的conf文件見http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/ex.hg.conf.

7. 建立緩存文件夾

rm /var/www/gw/trash mkdir /var/www/gw/trash chown www-data.www-data /var/www/gw/trash

8. 提供Javascript文件

mkdir -p /usr/local/apache/htdocs/ln -s /var/www/gw/js/ /usr/local/apache/htdocs/jsln -s /var/www/gw/style/ /usr/local/apache/htdocs/style # 每次重啟服務器后，可能要重復上述操作。

9. 這時就應該能夠訪問了，成功的標志就是訪問http://localhost/gw會看到UCSC常見的頁面。

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加載UCSC瀏覽器所需數據庫內容

1. 安裝hgcentral數據庫內容

wget http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql mysql -uroot -proot_passwd -e 'create database hgcentral' mysql -uroot -proot_passwd -e 'grant all privileges on hgcentral.* to 'gw'@'localhost'' # 加載下載的hgcentral數據庫 mysql -ugw -p qazplm_gw hgcentral <hgcentral.sql mysql -uroot -proot_passwd -e 'create database hgFixed' mysql -uroot -proot_passwd -e 'grant select on hgFixed.* to 'gw'@'localhost'

• 出現錯誤/var/www/gw/cgi-bin/hgGateway: error while loading shared libraries: libssl.so.6: cannot open shared object file: No such file or directory時的解決方案：

#如果不存在就安裝，如果存在就直接建立軟連接sudo apt-get install libssl0.9.8# Use `locate libssl.so.0.9.8` to find the path of this file. # For 32 bit ? sudo ln -s /lib/i386-linux-gnu/libssl.so.0.9.8 /usr/lib/libssl.so.6 ? sudo ln -s /lib/i386-linux-gnu/libcrypto.so.0.9.8 /usr/lib/libcrypto.so.

2. 獲取相關物種信息數據庫

# 鑒于物種信息數據庫比較大，可以在數據盤新建目錄用于存儲 #change datadir to /home/mysql /etc/init.d/mysql stop vim /etc/mysql/my.cnf#下載數據庫 rsync -avzP ?rsync://hgdownload.cse.ucsc.edu/mysql/mm9/chromInfo.MYD /home/mysql/mm9rsync -avzP rsync://hgdownload.cse.ucsc.edu/mysql/mm9/chromInfo.MYI /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/chromInfo.frm /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/cytoBandIdeo.MYD /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/cytoBandIdeo.MYI /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/cytoBandIdeo.frm /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/grp.MYD /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/grp.MYI /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/grp.frm /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/hgFindSpec.MYD /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/hgFindSpec.MYI /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/hgFindSpec.frm /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/trackDb.MYD /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/trackDb.MYI /home/mysql/mm9rsync -avzP ? rsync://hgdownload.cse.ucsc.edu/mysql/mm9/trackDb.frm /home/mysql/mm9 ##賦予權限 chown -R mysql.mysql /home/mysql/mm9

• 錯誤解決

  a. Could not connect to database (null) on localhost as gw. Client does not support authentication protocol requested by server; consider upgrading MySQL

  ?set password for 'gw'@'localhost'=OLD_PASSWORD('qazplm_gw');flush privileges;

  b. Cant connect to local MySQL server through socket ‘/var/lib/mysql/mysql.sock’

  ?ln -s /var/run/mysqld/mysqld.sock /var/lib/mysql/mysql.sockchmod 666 /var/lib/mysql/mysql.sockchmod 755 /var/lib/mysql/

3. 下載gbdb數據

#bbi 為encode數據 mkdir -p /home/user/gbdb/mm9 rsync -avzP --delete --max-delete=20 --exclude=bbi \ ? ? rsync://hgdownload.cse.ucsc.edu/gbdb/mm9/ ~/gbdb/mm9/ #---mappability data---------------rsync -avzp rsync://hgdownload.cse.ucsc.edu/gbdb/mm9/bbi/*.bw ~/gbdb/mm9/bbi ln -s /home/user/gbdb /gbdb

4. 訪問鏈接http://localhost/gw/cgi-bin/hgGateway?db=mm9

UCSC Track Hub使用

UCSC Track Hub可以方便加載多組高通量分析結果文件，并且可以使用Track overlay, 即不同的Track疊加到一起顯示，方便比較。具體見測序數據可視化 （三） - UCSC genomebrowser

1. 構建UCSC hub track

#首先看目錄結構 /var/www/hub$ tree . ├── genomes.txt ├── hub.txt └── mm9├── ctcf1.bw├── P3001.bw├── ctcf2.bw├── P3002.bw└── trackDb.txt#再看每個文件的內容 $cat genomes.txt genome mm9 trackDb mm9/trackDb.txt$cat hub.txt hub myhub shortLabel Testhub longLabel Testhubsdsdsdsd genomesFile genomes.txt email my@my.com$cat mm9/trackDb.txt # access http://localhost/cgi-bin/hgTracks?db=mm9&amp;hubUrl=https://localhost/hub.txt # help : http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html # trackDb.txt syntax http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigBed_-_Item_or_Region_Track_Settings #http://davetang.org/muse/2012/03/15/ucsc-genome-browser-custom-overlap-tracks/ track One container multiWig shortLabel One longLabel One type bigWig #viewLimits 0:160 visibility full aggregate transparentOverlay showSubtrackColorOnUi on priority 1.2 configurable on autoScale on dragAndDrop subtracks windowingFunction mean+whiskers maxHeightPixels 100:60:8track One_ctcf bigDataUrl ctcf1.bw shortLabel ctcf1.bw longLabel ctcf1.bw parent one type bigWig color 0,102,255track P300 bigDataUrl P3001.bw shortLabel P3001.bw longLabel P3001.bw parent one type bigWig color 136,102,255track Two container multiWig shortLabel Two longLabel Two type bigWig #viewLimits 0:160 visibility full aggregate transparentOverlay showSubtrackColorOnUi on windowingFunction maximum priority 1.2 configurable on autoScale on dragAndDrop subtrackstrack ctcf2 bigDataUrl ctcf2.bw shortLabel ctcf2.bw longLabel ctcf2.bw parent Two type bigWig color 0,102,255

2. 定時清理

#!/bin/bash #10080 means 10080 minutes which is 14 days. find /var/www/gw/trash/ \! \( -regex "/var/www/gw/trash/ct/.*" -or \-regex "/var/www/gw/trash/hgSs/.*" \) -type f -amin +10080 -exec rm -f {} \;

總結

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