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circos-software [2014/07/31 09:48] – created aorthcircos-software [2015/07/01 11:30] – aorth
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 ===== Usage ===== ===== Usage =====
  
-=== See versions of abyss which are available === +=== See versions of circos which are available === 
-<code>module avail abyss</code>+<code>$ module avail 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-0.66.tgz 
-tar zxf circos-0.66.tgz  +$ tar zxf circos-0.66.tgz  
-cd circos-0.66</code>+$ cd circos-0.66</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>+$ ./test.modules</code>
  
 For missing modules, check and install from system package manager first: 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</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</code>
  
 Install other modules manually: Install other modules manually:
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 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/0.66/{share,lib,lib64}/perl5 
-sudo chown -R aorth /export/apps/circos/0.66</code>+$ sudo chown -R aorth /export/apps/circos/0.66</code>
  
 Prepare CPAN for installing into our prefix: Prepare CPAN for installing into our prefix:
  
-<code>perl -e shell -MCPAN+<code>$ perl -e shell -MCPAN
 cpan[1]> o conf makepl_arg "INSTALLDIRS=site PREFIX=/export/apps/circos/0.66" 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[2]> o conf mbuildpl_arg "--prefix /export/apps/circos/0.66"
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 ===== 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/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 ./list.modules</code>
  
 Working! Working!
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 ===== Continue installation ===== ===== Continue installation =====
  
-<code>cd ~/src/circos-0.66 +<code>$ cd ~/src/circos-0.66 
-cp -r * /export/apps/circos/0.66</code>+$ cp -r * /export/apps/circos/0.66</code>
  
 ===== Try to run ===== ===== Try to run =====
 Add install dir to PATH and PERL5LIBS and try to run it: 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>$ 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): It might complain about more missing modules, so install them also (with CPAN like above):
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 ===== 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/0.66</code>
circos-software.txt · Last modified: 2022/11/28 08:10 by aorth