circos-software
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circos-software [2014/07/31 12:05] – aorth | circos-software [2020/09/18 09:59] – 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 modules one by one, ie: | + | |
- | < | + | Circos needs some Perl modules, check which we satisfy already with our Perl 5.28.2 package: |
- | ===== Test again ===== | + | < |
+ | $ cd bin | ||
+ | $ ./circos -modules</ | ||
- | < | + | Create directory for Perl modules |
- | Working! | + | < |
+ | $ sudo mkdir -p / | ||
+ | $ sudo chown -R aorth / | ||
+ | $ cpanm -l / | ||
+ | $ sudo yum install gd-devel | ||
+ | $ cpanm -l / | ||
+ | $ sudo yum remove gd-devel | ||
+ | $ cpanm -l / | ||
+ | $ cpanm -l / | ||
+ | </ | ||
- | ===== Continue installation ===== | + | Test again: |
- | < | + | < |
- | cp -r * /export/apps/circos/0.66</ | + | |
- | ===== 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: 2022/11/28 08:10 by aorth