我目前正在尝试在Ubuntu中安装Circos。
按照说明，我已转到bin文件夹并运行perl circos
我收到一个错误，告诉我没有安装一堆模块。 我尝试安装它们，除了两个之外，它们都有效。
当我进入cpan外壳时：
cpan[7]> install GD.pm
Running install for module 'GD'
LDS/GD-2.56.tar.gz
Has already been unwrapped into directory /home/qiime/.cpan/build/GD-2.56-DqDuWT
LDS/GD-2.56.tar.gz
'/usr/bin/perl Build.PL --installdirs site' returned status 512, not re-running
如果我从主终端运行它：
qiime@qiime-190-virtual-box:~/Documents/circos-0.69/bin$ perl -MCPAN -e 'install GD'
Reading '/home/qiime/.cpan/Metadata'
Database was generated on Wed, 27 Jan 2016 07:41:02 GMT
Running install for module 'GD'
Checksum for /home/qiime/.cpan/sources/authors/id/L/LD/LDS/GD-2.56.tar.gz ok
==> Couldn't mkdir '/home/qiime/.cpan/build/tmp-8161': Permission denied
==> Cannot continue: Please find the reason why I cannot make the <==
==> directory <==
==> /home/qiime/.cpan/build/tmp-8161 <==
==> and fix the problem, then retry. <==
每隔一个（总共~15个模块）模块安装没有问题。 我现在不确定该怎么做。 我想这是我错过的简单东西...？
为了完整起见，以下是尝试运行perl circos的错误：
qiime@qiime-190-virtual-box:~/Documents/circos-0.69/bin$ perl circos
*** REQUIRED MODULE(S) MISSING OR OUT-OF-DATE ***
You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial
http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules
missing GD
error Can't locate GD.pm in @INC (@INC contains: /home/qiime/Documents/circos-0.69/bin/lib /home/qiime/Documents/circos-0.69/bin/../lib /home/qiime/Documents/circos-0.69/bin /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at (eval 25) line 1.
missing GD::Polyline
error Can't locate GD/Polyline.pm in @INC (@INC contains: /home/qiime/Documents/circos-0.69/bin/lib /home/qiime/Documents/circos-0.69/bin/../lib /home/qiime/Documents/circos-0.69/bin /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at (eval 26) line 1.
编辑：更新我发现我可能没有安装libgd，所以我这样做了。 我尝试在 cpan shell 中运行 install GD.pm：
cpan[1]> install GD.pm
Reading '/home/qiime/.cpan/Metadata'
Database was generated on Wed, 27 Jan 2016 07:41:02 GMT
Running install for module 'GD'
Checksum for /home/qiime/.cpan/sources/authors/id/L/LD/LDS/GD-2.56.tar.gz ok
Scanning cache /home/qiime/.cpan/build for sizes
............................................................................DONE
Configuring L/LD/LDS/GD-2.56.tar.gz with Build.PL
Configuring for libgd version 2.0.36.
Checking for stray libgd header files...none found.
Unknown option: installdirs
Usage: perl Build.PL [options]
Configure GD module.
Options:
-options "JPEG,FT,PNG,GIF,XPM,ANIMGIF" feature options, separated by commas
-lib_gd_path path path to libgd
-lib_ft_path path path to Freetype library
-lib_png_path path path to libpng
-lib_jpeg_path path path to libjpeg
-lib_xpm_path path path to libxpm
-lib_zlib_path path path to libpng
-ignore_missing_gd Ignore missing or old libgd installations and try to compile anyway
If no options are passed on the command line. The program will
attempt to autoconfigure itself with the gdlib-config program (present
in GD versions 2.0.27 or later). Otherwise it will prompt for these
values interactively.
Warning: No success on command[/usr/bin/perl Build.PL --installdirs site]
LDS/GD-2.56.tar.gz
/usr/bin/perl Build.PL --installdirs site -- NOT OK
Failed during this command:
LDS/GD-2.56.tar.gz : writemakefile NO '/usr/bin/perl Build.PL --installdirs site' returned status 512
正如 G. Cito 所建议的，perl 中的 GD 模块存在问题。
我使用了他发布的说明以及以下内容来修复错误：
- 无法使用 cpan 在达尔文 13.0.1 上安装 GD 模块
- 在 OS X 上安装 Circos
具体来说，最后一段代码是我为 perl 正确安装 GD 模块所需要的：
srctemp$ curl -O http://www.cpan.org/authors/id/L/LD/LDS/GD-2.49.tar.gz (if curl fails copy and past on your browser)
srctemp$ tar -xzvf GD-2.49.tar.gz
srctemp$ cd GD-2.49
srctemp/GD-2.49$ perl Makefile.PL
srctemp/GD-2.49$ make
srctemp/GD-2.49$ sudo make install
这本身并不是一个真正的修复程序，但请查看：
- 无法使用 cpan 在达尔文 13.0.1 上安装 GD 模块