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circos-software
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circos-software [2015/07/01 11:30] aorth |
circos-software [2020/09/18 10:00] aorth |
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| ===== Information ===== | ===== Information ===== | ||
| - | * Version: 0.66 | + | * Version: 0.69-9 |
| * Added: July, 2014 | * Added: July, 2014 | ||
| + | * Updated: September, 2020 | ||
| * Link: http:// | * Link: http:// | ||
| ===== Usage ===== | ===== Usage ===== | ||
| - | === See versions of circos which are available | + | See versions of circos which are available: |
| < | < | ||
| + | |||
| + | Load one version into your environment and run it: | ||
| + | < | ||
| + | $ circos</ | ||
| ===== Installation ====== | ===== Installation ====== | ||
| Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
| - | < | + | < |
| - | $ tar zxf circos-0.66.tgz | + | $ wget http:// |
| - | $ cd circos-0.66</ | + | $ tar zxf circos-0.69-9.tgz |
| - | + | $ cd circos-0.69-9</ | |
| - | ===== Check requirements ===== | + | |
| - | Circos needs some perl modules, check which we satisfy already: | + | |
| - | + | ||
| - | < | + | |
| - | $ ./ | + | |
| - | + | ||
| - | For missing modules, check and install from system package manager first: | + | |
| - | + | ||
| - | < | + | |
| - | + | ||
| - | Install other modules manually: | + | |
| - | + | ||
| - | < | + | |
| - | Math:: | + | |
| - | + | ||
| - | ===== Install missing perl modules ===== | + | |
| - | Create directories for perl modules: | + | |
| - | + | ||
| - | < | + | |
| - | $ sudo chown -R aorth / | + | |
| - | + | ||
| - | Prepare CPAN for installing into our prefix: | + | |
| - | + | ||
| - | < | + | |
| - | cpan[1]> o conf makepl_arg " | + | |
| - | cpan[2]> o conf mbuildpl_arg " | + | |
| - | cpan[3]> o conf commit</ | + | |
| - | Then install the missing | + | Circos needs some Perl modules, |
| - | < | + | < |
| + | $ cd bin | ||
| + | $ ./circos -modules</ | ||
| - | ===== Test again ===== | + | Create directory for Perl modules and install missing modules with cpanm: |
| - | < | + | < |
| + | $ sudo mkdir -p / | ||
| + | $ sudo chown -R aorth / | ||
| + | $ cpanm -l / | ||
| + | $ sudo yum install gd-devel | ||
| + | $ cpanm -l / | ||
| + | $ sudo yum remove gd-devel | ||
| + | $ cpanm -l /export/ | ||
| + | $ cpanm -l / | ||
| + | </ | ||
| - | 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: |
| - | < | + | < |
| - | $ cp -r * / | + | |
| - | ===== Try to run ===== | + | When all module requirements are satisfied continue the installation: |
| - | Add install dir to PATH and PERL5LIBS and try to run it: | + | |
| - | < | + | < |
| + | $ cp -r * / | ||
| - | It might complain about more missing modules, so install | + | Add install |
| - | < | + | < |
| - | Set:: | + | $ export PERL5LIB=$PERL5LIB:/ |
| + | $ circos -modules</ | ||
| - | ===== Fix permissions | + | Fix permissions: |
| - | < | + | < |
circos-software.txt · Last modified: 2020/09/18 10:14 by aorth
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