dna配置数据源mysql_本地安装UCSC基因组浏览器

UCSC基因组浏览器在大规模高通量数据的可视化和比较分析研究中发挥着重要的作用。拥有了本地浏览器，就可以对自己的测序数据进行更深入的分析和共享使用。本文详细介绍了如何一步步在本地安装、配置、高级使用UCSC浏览器。

安装UCSC浏览器

1. 安装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用户

# 用户名：gw

# 密码 ：qazplm_gw

create user 'gw'@'localhost' identified by 'qazplm_gw';

3. 同步UCSC所需html文件和运行程序

# 设置UCSC的安装目录为 /var/www/gw

mkdir /var/www/gw

# 同步相应的html文件

rsync -avzP --exclude 'ENCODE' rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/gw

# 同步可执行程序到cgi-bin目录下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目录的所有者

chown -R www-data.www-data /var/www/gw/cgi-bin/

4. 把以下内容写入/etc/apahce2/httpd.conf

# XBitHack on 是必须的

# 其它参数的意思参见apache文档

XBitHack on

AllowOverride AuthConfig

Options +Includes

# the ScriptAlias directive is crucial

ScriptAlias /gw/cgi-bin /var/www/gw/cgi-bin

AllowOverride None

Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch

Order allow,deny

Allow from all

AddHandler cgi-script cgi pl

5. 设置Apache解析有执行权限的文件中的SSI指令，然后重启apache

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

6. 设置数据库配置文件

进入/var/www/gw/cgi-bin/目录，建立hg.conf文件并写入下列内容

db.host=localhost

db.user=gw

db.password=qazplm_gw

db.trackDb=trackDb

central.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=

同时运行如下命令sudo chown www-data /var/www/gw/cgi-bin/hg.conf更改文件的所有权。

7. 建立缓存文件夹

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

# 每次重启服务器后，可能要重复上述操作。

9. 这时就应该能够访问了，成功的标志就是访问http://localhost/gw会看到UCSC常见的页面。

加载UCSC浏览器所需数据库内容

1. 安装hgcentral数据库内容

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''

# 加载下载的hgcentral数据库

mysql -ugw -p qazplm_gw hgcentral

mysql -uroot -proot_passwd -e 'create database hgFixed'

mysql -uroot -proot_passwd -e 'grant select on hgFixed.* to 'gw'@'localhost'

出现错误/var/www/gw/cgi-bin/hgGateway: error while loading shared libraries: libssl.so.6: cannot open shared object file: No such file or directory时的解决方案：

#如果不存在就安装，如果存在就直接建立软连接

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. 获取相关物种信息数据库

# 鉴于物种信息数据库比较大，可以在数据盘新建目录用于存储

#change datadir to /home/mysql

/etc/init.d/mysql stop

vim /etc/mysql/my.cnf

#下载数据库

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

##赋予权限

chown -R mysql.mysql /home/mysql/mm9

错误解决

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.sock

chmod 666 /var/lib/mysql/mysql.sock

chmod 755 /var/lib/mysql/

3. 下载gbdb数据

#bbi 为encode数据

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

UCSC Track Hub使用

UCSC Track Hub可以方便加载多组高通量分析结果文件，并且可以使用Track overlay, 即不同的Track叠加到一起显示，方便比较。具体见测序数据可视化 (三) - UCSC genomebrowser

1. 构建UCSC hub track

#首先看目录结构

/var/www/hub$ tree

.

├── genomes.txt

├── hub.txt

└── mm9

├── ctcf1.bw

├── P3001.bw

├── ctcf2.bw

├── P3002.bw

└── trackDb.txt

#再看每个文件的内容

$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&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 100:60:8

track One_ctcf

bigDataUrl ctcf1.bw

shortLabel ctcf1.bw

longLabel ctcf1.bw

parent one

type bigWig

color 0,102,255

track P300

bigDataUrl P3001.bw

shortLabel P3001.bw

longLabel P3001.bw

parent one

type bigWig

color 136,102,255

track 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 subtracks

track ctcf2

bigDataUrl ctcf2.bw

shortLabel ctcf2.bw

longLabel ctcf2.bw

parent Two

type bigWig

color 0,102,255

2. 定时清理

#!/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 {} \;