Linux下软件安装：Circos

Linux下安装Circos

1. 下载源码包并解压

wget http://circos.ca/distribution/circos-0.69-9.tgz
tar -xvfz circos-0.69-9
cd circos-0.69-9/
chmod -x bin/circos

2. 查看所需的perl模块，并测试circos是否可以直接运行。如果报错，那么按要求安装对应的perl模块。

cd bin/
./list.modules ## 查看程序运行所需的perl模块
./circos -v ## 如果报错，那么大概率是因为对应模块没有安装，现用cpanm安装perl 模块

3. 安装cpanm

mkdir tempFolder ## 新建任意目录
wget http://xrl.us/cpanm --no-check-certificate -O /tempFolder/cpanm ## 将cpanm下载到该目录下
chmod 777 cpanm  ## 赋予执行权限

4. 用cpanm安装perl模块

sudo ./cpanm 模块名称

模块名称：
Carp   
Clone
Config::General
Cwd   
Data::Dumper   
Digest::MD5  
File::Basename 
File::Spec::Functions   
File::Temp  
FindBin   
Font::TTF::Font   
GD 
GD::Polyline   
Getopt::Long   
IO::File   
List::MoreUtils
List::Util   
Math::Bezier
Math::BigFloat   
Math::Round   
Math::VecStat   
Memoize   
POSIX   
Params::Validate   
Pod::Usage   
Readonly  
Regexp::Common  
SVG   
Set::IntSpan   
Statistics::Basic   
Storable
Sys::Hostname    
Text::Balanced  
Text::Format   
Time::HiRes

5. 以Circos官网提供的示例进行测试

1.在Linux的circos-0.69-9中新建mycircos文件夹mkdir mycircos，在该文件夹中新建circos.conf文件、ideogram.conf文件和ticks.conf文件touch circos.conf ideogram.conf ticks.conf。
2.三个conf代码如下（从官网获取即可）

#circos.conf
karyotype = data/karyotype/karyotype.human.txt

chromosomes_units = 1000000

<<include ideogram.conf>>

<<include ticks.conf>>

<image>
<<include etc/image.conf>>                
</image>

<<include etc/colors_fonts_patterns.conf>> 

<<include etc/housekeeping.conf>>

#ideogram.conf
<ideogram>

<spacing>
default = 0.005r
</spacing>

radius           = 0.90r
thickness        = 20p
fill             = yes
stroke_color     = dgrey
stroke_thickness = 2p

show_label       = yes

label_font       = default 
label_radius     = dims(image,radius) - 60p
label_size       = 30
label_parallel   = yes

</ideogram>

#ticks.conf
show_ticks          = yes
show_tick_labels    = yes
<ticks>
radius           = 1r
color            = black
thickness        = 2p
multiplier       = 1e-6
format           = %d

<tick>
spacing        = 5u
size           = 10p
</tick>

<tick>
spacing        = 25u
size           = 15p
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
</tick>

</ticks>

3. 测试
终端中切换到circos所在目录，并运行：

./circos –conf ../mycircos/circos.conf