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circos-software [2020/09/18 08:40] – aorthcircos-software [2022/11/28 08:10] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 0.69.9+  * Version: 0.69-9
   * Added: July, 2014   * Added: July, 2014
-  * Updated: April, 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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 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ wget http://circos.ca/distribution/circos-0.69-9.tgz+<code>$ cd /tmp 
 +$ wget http://circos.ca/distribution/circos-0.69-9.tgz
 $ tar zxf circos-0.69-9.tgz $ tar zxf circos-0.69-9.tgz
 $ cd circos-0.69-9</code> $ cd circos-0.69-9</code>
  
-===== Check requirements ===== +Circos needs some Perl modules, check which we satisfy already with our system Perl:
-Circos needs some Perl modules, check which we satisfy already:+
  
-<code>$ cd bin +<code>$ ./bin/circos -modules</code>
-$ ./circos -modules</code>+
  
-For missing modules, check and install from the system package manager first: +Create a directory for custom Perl modules and install missing modules with cpanm:
- +
-<code>$ yum install perl-Clone.x86_64 perl-Config-General.noarch perl-Font-TTF.noarch perl-Readonly.noarch perl-Regexp-Common.noarch perl-Text-Format.noarch perl-Math-Round</code> +
- +
-Install any other missing modules manually using ''cpanm'': +
- +
-  * ''Math::Bezier'' +
-  * ''Math::VecStat'' +
-  * ''SVG'' +
-  * ''Set::IntSpan'' +
- +
-===== Install missing perl modules ===== +
-Create directories for perl modules:+
  
 <code>$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5 <code>$ 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/ Math::Bezier +$ cpanm -l /export/apps/circos/0.69-9 Math::Bezier Math::VecStat SVG Set::IntSpan</code>
-...</code>+
  
-===== 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>
  
-===== Continue 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>
  
-===== Try to run ===== 
 Add install directory to PATH and PERL5LIB and try to run it: Add install directory to PATH and PERL5LIB and try to run it:
  
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 $ circos -modules</code> $ circos -modules</code>
  
-===== Fix permissions =====+Fix permissions:
  
 <code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code> <code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code>
circos-software.1600418405.txt.gz · Last modified: by aorth