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circos-software [2015/07/01 11:30] aorthcircos-software [2020/09/18 08:40] aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 0.66+  * Version: 0.69.9
   * Added: July, 2014   * Added: July, 2014
 +  * Updated: April, 2020
   * Link: http://circos.ca/   * Link: http://circos.ca/
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of circos which are available ===+See versions of circos which are available:
 <code>$ module avail circos</code> <code>$ module avail circos</code>
 +
 +Load one version into your environment and run it:
 +<code>$ module load circos/0.69-9
 +$ circos</code>
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ wget http://circos.ca/distribution/circos-0.66.tgz +<code>$ wget http://circos.ca/distribution/circos-0.69-9.tgz 
-$ tar zxf circos-0.66.tgz  +$ tar zxf circos-0.69-9.tgz 
-$ cd circos-0.66</code>+$ cd circos-0.69-9</code>
  
 ===== Check requirements ===== ===== Check requirements =====
-Circos needs some perl modules, check which we satisfy already:+Circos needs some Perl modules, check which we satisfy already:
  
 <code>$ cd bin <code>$ cd bin
-$ ./test.modules</code>+$ ./circos -modules</code>
  
-For missing modules, check and install from system package manager first:+For missing modules, check and install from the system package manager first:
  
-<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</code>+<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 other modules manually:+Install any other missing modules manually using ''cpanm'':
  
-<code>Math::Round +  * ''Math::Bezier'' 
-Math::VecStat</code>+  * ''Math::VecStat'' 
 +  * ''SVG'' 
 +  * ''Set::IntSpan''
  
 ===== Install missing perl modules ===== ===== Install missing perl modules =====
 Create directories for perl modules: Create directories for perl modules:
  
-<code>$ sudo mkdir -p /export/apps/circos/0.66/{share,lib,lib64}/perl5 +<code>$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5 
-$ sudo chown -R aorth /export/apps/circos/0.66</code> +$ sudo chown -R aorth /export/apps/circos/0.69-9 
- +cpanm -/export/apps/circos/0.69-9/ Math::Bezier 
-Prepare CPAN for installing into our prefix: +...</code>
- +
-<code>perl -e shell -MCPAN +
-cpan[1]> o conf makepl_arg "INSTALLDIRS=site PREFIX=/export/apps/circos/0.66" +
-cpan[2]> o conf mbuildpl_arg "--prefix /export/apps/circos/0.66" +
-cpan[3]> o conf commit</code> +
- +
-Then install the missing modules one by one, ie: +
- +
-<code>install Math::Round</code>+
  
 ===== Test again ===== ===== Test again =====
  
-<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 ./list.modules</code> +<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>
- +
-Working!+
  
 ===== Continue installation ===== ===== Continue installation =====
  
-<code>$ cd ~/src/circos-0.66 +<code>$ cd /tmp/src/circos-0.69-9 
-$ cp -r * /export/apps/circos/0.66</code>+$ cp -r * /export/apps/circos/0.69-9</code>
  
 ===== Try to run ===== ===== Try to run =====
-Add install dir to PATH and PERL5LIBS and try to run it+Add install directory to PATH and PERL5LIB and try to run it:
- +
-<code>$ PATH=$PATH:/export/apps/circos/0.66/bin $ PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 circos</code> +
- +
-It might complain about more missing modules, so install them also (with CPAN like above):+
  
-<code>Math::Bezier +<code>$ export PATH=$PATH:/export/apps/circos/0.69-9/bin 
-Set::IntSpan</code>+$ export PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 
 +$ circos -modules</code>
  
 ===== Fix permissions ===== ===== Fix permissions =====
  
-<code>$ sudo chown -R root:root /export/apps/circos/0.66</code>+<code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code>
circos-software.txt · Last modified: 2022/11/28 08:10 by aorth