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circos-software [2020/04/07 13:28]
circos-software [2020/09/18 10:14]
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 ===== Information ===== ===== Information =====
-  * Version: 0.67+  * Version: 0.69-9
   * Added: July, 2014   * Added: July, 2014
-  * Updated: August2015+  * Updated: September2020
   * Link:   * Link:
 ===== 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 +<code>$ cd /tmp 
-$ tar zxf circos-0.69-9.tgz  +$ wget 
-$ cd circos-0.66-9</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 with our Perl 5.28.2 package:
-Circos needs some Perl modules, check which we satisfy already:+
-<code>cd bin +<code>module load perl/5.28.2 
-$ ./circos -modules</code>+$ ./bin/circos -modules</code>
-For missing modules, check and install from the system package manager first:+Create directory for 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>+<code> 
 +sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5 
 +$ sudo chown -R aorth /export/apps/circos/0.69-
 +$ cpanm -l /export/apps/circos/0.69-9/ Clone Config::General Font::TTF::Font 
 +$ sudo yum install gd-devel 
 +$ cpanm -l /export/apps/circos/0.69-9/ 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 
-Install any other missing modules manually using ''cpanm'': +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.
- +
-  * ''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 +
-$ sudo chown -R aorth /export/apps/circos/0.69-9 +
-$ cpanm -l /export/apps/circos/0.69-9/ Math::Bezier +
-===== Test again =====+Test again:
 <code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code> <code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>
-===== Continue installation =====+When all module requirements are satisfied continue the installation:
 <code>$ cd /tmp/src/circos-0.69-9 <code>$ cd /tmp/src/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.txt · Last modified: 2020/09/18 10:14 by aorth