circos學習筆記(一):Mac版本安裝circos及驗證是否可用

1,下載circos,http://circos.ca/software/download/circos/,放置到常用文件夾;

2,選擇文件中的circos命令,並添加到Mac的bin文件夾中,使得circos命令可用,類似於pip、conda等命令,如下圖:

添加方法:

                   已知circos文件如下:

                               

                   終端執行命令:

                               export PATH=$PATH:`pwd`/circos-0.69-9/bin

3,終端使用,列出circos依賴的Perl包命令:circos -module

上圖僅顯示部分module結果;

4,若顯示missing,則需安裝;

先進去:perl -MCPAN -e shell

安裝module:install XXX

5,最簡單出圖
      把下面的內容存儲到任意目錄下的任意文件比如ehbio.conf下,然後運行circos -conf ehbio.conf就可以獲得circos的圖circos.png和circos.svg。(建議在終端常用工作目錄中使用circos命令)

ehbio.conf內容(引用如下):

karyotype = data/karyotype/karyotype.human.txt

<ideogram>

<spacing>
default = 0.005r
</spacing>

radius    = 0.9r
thickness = 20p
fill      = yes

</ideogram>

################################################################
# The remaining content is standard and required. It is imported 
# from default files in the Circos distribution.
#
# These should be present in every Circos configuration file and
# overridden as required. To see the content of these files, 
# look in etc/ in the Circos distribution.

<image>
# Included from Circos distribution.
<<include etc/image.conf>>
</image>

# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
# Included from Circos distribution.
<<include etc/colors_fonts_patterns.conf>>

# Debugging, I/O an dother system parameters
# Included from Circos distribution.
<<include etc/housekeeping.conf>>

6,結果顯示如下即可:

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