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circos-software [2020/09/18 10:14] – aorthcircos-software [2022/11/28 08:10] (current) – aorth
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   * Version: 0.69-9   * Version: 0.69-9
   * Added: July, 2014   * Added: July, 2014
-  * Updated: September, 2020+  * Updated: November, 2022
   * Link: http://circos.ca/   * Link: http://circos.ca/
  
 ===== Usage ===== ===== Usage =====
  
-See versions of circos which are available:+See versions which are available:
 <code>$ module avail circos</code> <code>$ module avail circos</code>
  
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 $ cd circos-0.69-9</code> $ cd circos-0.69-9</code>
  
-Circos needs some Perl modules, check which we satisfy already with our Perl 5.28.2 package:+Circos needs some Perl modules, check which we satisfy already with our system Perl:
  
-<code>$ module load perl/5.28.2 +<code>$ ./bin/circos -modules</code>
-$ ./bin/circos -modules</code>+
  
-Create directory for Perl modules and install missing modules with cpanm:+Create a directory for custom Perl modules and install missing modules with cpanm:
  
-<code> +<code>$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5
-$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5+
 $ sudo chown -R aorth /export/apps/circos/0.69-9 $ sudo chown -R aorth /export/apps/circos/0.69-9
-$ cpanm -l /export/apps/circos/0.69-9/ Clone Config::General Font::TTF::Font +$ cpanm -l /export/apps/circos/0.69-9 Math::Bezier Math::VecStat SVG Set::IntSpan</code>
-$ sudo yum install gd-devel +
-$ cpanm -l /export/apps/circos/0.69-9/ GD GD::Polyline +
-$ sudo yum remove gd-devel +
-$ cpanm -l /export/apps/circos/0.69-9/ List::MoreUtils Math::Bezier Math::Round Math::VecStat +
-$ cpanm -l /export/apps/circos/0.69-9/ Params::Validate Readonly Regexp::Common SVG Set::IntSpanStatistics::Basic Text::Format +
-</code> +
- +
-I don't install all the missing modules at once because sometimes they have errors and it's easier to track them down when you do less in one go.+
  
 Test again: Test again:
  
-<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>+<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./bin/circos -modules</code>
  
 When all module requirements are satisfied continue the installation: When all module requirements are satisfied continue the installation:
  
-<code>$ cd /tmp/src/circos-0.69-9+<code>$ cd /tmp/circos-0.69-9
 $ cp -r * /export/apps/circos/0.69-9</code> $ cp -r * /export/apps/circos/0.69-9</code>
  
circos-software.txt · Last modified: 2022/11/28 08:10 by aorth