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circos-software [2020/04/07 12:54]
aorth
circos-software [2020/09/18 10:14] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 0.67+  * Version: 0.69-9
   * Added: July, 2014   * Added: July, 2014
-  * Updated: August2015+  * Updated: September2020
   * 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>$ cd /tmp 
-$ tar zxf circos-0.66.tgz  +$ wget http://circos.ca/distribution/circos-0.69-9.tgz 
-$ cd circos-0.66</code> +$ tar zxf circos-0.69-9.tgz 
- +$ cd circos-0.69-9</code>
-===== Check requirements ===== +
-Circos needs some perl modules, check which we satisfy already: +
- +
-<code>$ cd bin +
-$ ./test.modules</code> +
- +
-For missing modules, check and install from 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 perl-Math-Round</code> +
- +
-Install any other missing modules manually: +
- +
-- ''Math::Bezier'' +
-- ''Math::VecStat'' +
-- ''SVG'' +
-- ''Set::IntSpan'' +
- +
-===== Install missing perl modules ===== +
-Create directories for perl modules: +
- +
-<code>$ sudo mkdir -p /export/apps/circos/0.66/{share,lib,lib64}/perl5 +
-$ sudo chown -R aorth /export/apps/circos/0.66</code> +
- +
-Prepare CPAN for installing into our prefix: +
- +
-<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 oneie:+Circos needs some Perl modules, check which we satisfy already with our Perl 5.28.2 package:
  
-<code>install Math::Round</code>+<code>$ module load perl/5.28.2 
 +$ ./bin/circos -modules</code>
  
-===== Test again =====+Create directory for Perl modules and install missing modules with cpanm:
  
-<code>PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 ./list.modules</code>+<code> 
 +sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5 
 +$ sudo chown -R aorth /export/apps/circos/0.69-9 
 +$ cpanm -l /export/apps/circos/0.69-9/ Clone Config::General Font::TTF::Font 
 +$ sudo yum install gd-devel 
 +$ cpanm -l /export/apps/circos/0.69-9GD GD::Polyline 
 +$ sudo yum remove gd-devel 
 +$ cpanm -l /export/apps/circos/0.69-9List::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>
  
-Working!+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.
  
-===== Continue installation =====+Test again:
  
-<code>cd ~/src/circos-0.66 +<code>PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>
-cp -r * /export/apps/circos/0.66</code>+
  
-===== Try to run ===== +When all module requirements are satisfied continue the installation:
-Add install dir to PATH and PERL5LIBS 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>+<code>cd /tmp/src/circos-0.69-9 
 +cp -r * /export/apps/circos/0.69-9</code>
  
-It might complain about more missing modules, so install them also (with CPAN like above):+Add install directory to PATH and PERL5LIB and try to run it:
  
-<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.1586264092.txt.gz · Last modified: 2020/04/07 12:54 by aorth