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。 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

代码语言：javascript复制

#For Ubuntu user
sudo apt-get install tasksel
sudo apt-get install lamp-server

#For readhat or centos user
yum install httpd mariadb-server mariadb

2. 新建mysql用户

代码语言：javascript复制

# 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

代码语言：javascript复制

# 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

# For 32-it
rsync -avzP rsync://hgdownload.cse.ucsc.edu/cgi-bin-i386/ /var/www/gw/cgi-bin/  #32bit

# 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

代码语言：javascript复制

/etc/apache2$ cat httpd.conf
# XBitHack on 是必须的
# 其它参数的意思参见apache文档
XBitHack on
<Directory /var/www/gw>
    AllowOverride AuthConfig
    Options  Includes
</Directory>

 # the ScriptAlias directive is crucial

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

<Directory "/var/www/gw/cgi-bin">

    AllowOverride None
    Options  ExecCGI -MultiViews  SymLinksIfOwnerMatch

    Order allow,deny
    Allow from all
    AddHandler cgi-script cgi pl

</Directory>

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

代码语言：javascript复制

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

代码语言：javascript复制

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。

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

7. 建立缓存文件夹

代码语言：javascript复制

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

代码语言：javascript复制

mkdir -p /usr/local/apache/htdocs/
ln -s /var/www/gw/js/ /usr/local/apache/htdocs/js
ln -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

代码语言：javascript复制

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 <hgcentral.sql
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.6

2. 获取相关物种信息数据库

代码语言：javascript复制

# 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/mm10/chromInfo.MYD /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chromInfo.MYI /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chromInfo.frm /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/cytoBandIdeo.MYD /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/cytoBandIdeo.MYI /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/cytoBandIdeo.frm /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/grp.MYD /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/grp.MYI /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/grp.frm /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/hgFindSpec.MYD /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/hgFindSpec.MYI /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/hgFindSpec.frm /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/trackDb.MYD /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/trackDb.MYI /home/mysql/mm10
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/trackDb.frm /home/mysql/mm10

##赋予权限
chown -R mysql.mysql /home/mysql/mm10

• 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

代码语言：javascript复制

#bbi 为encode数据
mkdir -p /home/user/gbdb/mm10
rsync -avzP --delete --max-delete=20 --exclude=bbi 
    rsync://hgdownload.cse.ucsc.edu/gbdb/mm10/ ~/gbdb/mm10/
#---mappability data---------------
rsync -avzp rsync://hgdownload.cse.ucsc.edu/gbdb/mm10/bbi/*.bw ~/gbdb/mm10/bbi
ln -s /home/user/gbdb /gbdb

4. 访问链接http://localhost/gw/cgi-bin/hgGateway?db=mm10

5. 安装参考：

• http://blog.sciencenet.cn/blog-723745-569746.html
• http://enotacoes.wordpress.com/2009/09/03/installing-a-minimal-ucsc-mirror-in-ubuntu-jaunty-64-bits/

---

UCSC Track Hub使用

1. 构建UCSC hub track

代码语言：javascript复制

#首先看目录结构
/var/www/hub$ tree
.
├── genomes.txt
├── hub.txt
└── mm10
    ├── ctcf1.bw
    ├── P3001.bw
    ├── ctcf2.bw
    ├── P3002.bw
    └── trackDb.txt

1 directory, 7 files

#再看每个文件的内容
$cat genomes.txt
genome    mm10
trackDb    mm10/trackDb.txt

$cat hub.txt
hub    myhub
shortLabel    Testhub
longLabel    Testhubsdsdsdsd
genomesFile    genomes.txt
email    my@my.com

$cat mm10/trackDb.txt
# access http://localhost/cgi-bin/hgTracks?db=mm10&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

track P3002
bigDataUrl P3002.bw
shortLabel P3002.bw
longLabel P3002.bw
parent Two
type bigWig
color 136,102,255

---

其它需要添加的数据

1. mm10相关数据表

代码语言：javascript复制

rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/all_bacends.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/all_bacends.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/all_bacends.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chromInfo.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chromInfo.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chromInfo.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/cytoBandIdeo.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/cytoBandIdeo.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/cytoBandIdeo.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/description.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/description.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/description.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/downloadlist.txt /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/extFile.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/extFile.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/extFile.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbCdnaInfo.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbCdnaInfo.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbCdnaInfo.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbExtFile.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbExtFile.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbExtFile.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbLoaded.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbLoaded.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbLoaded.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbMiscDiff.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbMiscDiff.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbMiscDiff.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbSeq.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbSeq.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbSeq.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbStatus.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbStatus.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbStatus.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbWarn.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbWarn.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/gbWarn.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/grp.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/grp.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/grp.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/hgFindSpec.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/hgFindSpec.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/hgFindSpec.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/history.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/history.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/history.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgAlias.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgAlias.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgAlias.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgColor.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgColor.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgColor.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgProtAlias.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgProtAlias.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgProtAlias.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgProtMap2.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgProtMap2.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgProtMap2.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgSpAlias.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgSpAlias.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgSpAlias.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgTargetAli.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgTargetAli.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgTargetAli.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgTxInfo.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgTxInfo.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgTxInfo.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgXref.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgXref.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/kgXref.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownAlt.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownAlt.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownAlt.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownBlastTab.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownBlastTab.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownBlastTab.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownCanonical.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownCanonical.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownCanonical.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGene.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGeneMrna.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGeneMrna.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGeneMrna.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGene.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGene.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGenePep.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGenePep.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownGenePep.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownIsoforms.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownIsoforms.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownIsoforms.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToAllenBrain.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToAllenBrain.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToAllenBrain.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToEnsembl.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToEnsembl.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToEnsembl.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToGnf1m.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToGnf1m.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToGnf1m.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToGnfAtlas2.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToGnfAtlas2.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToGnfAtlas2.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToLocusLink.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToLocusLink.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToLocusLink.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToMOE430A.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToMOE430A.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToMOE430A.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToMOE430.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToMOE430.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToMOE430.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToPfam.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToPfam.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToPfam.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToRefSeq.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToRefSeq.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToRefSeq.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToSuper.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToSuper.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToSuper.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToU74.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToU74.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToU74.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToVisiGene.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToVisiGene.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/knownToVisiGene.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/microsat.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/microsat.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/microsat.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30wayFrames.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30wayFrames.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30wayFrames.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30way.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30way.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30way.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30waySummary.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30waySummary.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/multiz30waySummary.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/pfamDesc.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/pfamDesc.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/pfamDesc.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30wayEuarch.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30wayEuarch.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30wayEuarch.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30way.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30way.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30way.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30wayPlacental.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30wayPlacental.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastCons30wayPlacental.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30wayEuarch.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30wayEuarch.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30wayEuarch.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30way.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30way.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30way.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30wayPlacental.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30wayPlacental.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/phastConsElements30wayPlacental.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refFlat.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refFlat.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refFlat.MYD.1 /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refFlat.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refGene.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refGene.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refGene.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refLink.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refLink.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refLink.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqAli.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqAli.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqAli.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqStatus.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqStatus.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqStatus.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqSummary.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqSummary.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/refSeqSummary.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/scopDesc.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/scopDesc.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/scopDesc.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/simpleRepeat.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/simpleRepeat.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/simpleRepeat.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/tableDescriptions.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/tableDescriptions.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/tableDescriptions.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/trackDb.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/trackDb.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/trackDb.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/ucscScop.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/ucscScop.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/ucscScop.MYI /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/organism* /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chr*_rmsk.frm /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chr*_rmsk.MYD /home/mysql/mm10/
rsync -avzP  rsync://hgdownload.cse.ucsc.edu/mysql/mm10/chr*_rmsk.MYI /home/mysql/mm10/

2. 定时清理

代码语言：javascript复制

#!/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 {} ;

3. 其它基因组浏览器

• Trackster http://epigenomegateway.wustl.edu/browser/
• IGV

---

UCSC输出eps或pdf

1. To print or save the image to a file:
   • In the blue navigation bar at the top of the screen, from the View menu, click the PDF/PS link.
2. One can get to the page where you can export .eps files by altering your URL.
   • If you add hgGenome_doPsOutput=1 right after the ? and add an & right after it, you should get to the PostScript/PDF Output screen.
   • Your altered URL will look something like this: http://genome.ucsc.edu/cgi-bin/hgGenome?hgGenome_doPsOutput=1&hgsid=301123643&clade=mammal&org=Human&db=hg19&hgGenome_threshold_hg19=3.5&hgGenome_graph_hg19_1_1=ct_UserTrack1_8429&hgGenome_graphColor_hg19_1_1=blue&hgGenome_graph_hg19_1_2=&hgGenome_graphColor_hg19_1_2=red.

云数据库SQLServer apache 互联网医疗

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