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circos-software [2015/08/20 15:52]
joguya
circos-software [2020/04/07 16:36] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 0.67+  * Version: 0.69.9
   * Added: July, 2014   * Added: July, 2014
-  * Updated: ​August2015+  * Updated: ​April2020
   * 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-0.66-9</​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.1440075120.txt.gz · Last modified: 2015/08/20 15:52 by joguya