{"id":21925539,"url":"https://github.com/node/circos","last_synced_at":"2025-04-19T15:47:56.343Z","repository":{"id":9119233,"uuid":"10904378","full_name":"node/circos","owner":"node","description":" Mirror of cricos.  \"Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. \"","archived":false,"fork":false,"pushed_at":"2023-04-20T03:08:41.000Z","size":57889,"stargazers_count":8,"open_issues_count":0,"forks_count":12,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-29T09:34:14.407Z","etag":null,"topics":["circos","data","visualization"],"latest_commit_sha":null,"homepage":"http://circos.ca","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/node.png","metadata":{"files":{"readme":"README","changelog":"CHANGES","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION","codeowners":null,"security":null,"support":"SUPPORT"}},"created_at":"2013-06-24T09:49:11.000Z","updated_at":"2023-05-19T15:03:46.000Z","dependencies_parsed_at":"2022-07-09T23:00:31.237Z","dependency_job_id":null,"html_url":"https://github.com/node/circos","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/node%2Fcircos","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/node%2Fcircos/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/node%2Fcircos/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/node%2Fcircos/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/node","download_url":"https://codeload.github.com/node/circos/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249730581,"owners_count":21317327,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["circos","data","visualization"],"created_at":"2024-11-28T21:19:08.983Z","updated_at":"2025-04-19T15:47:56.327Z","avatar_url":"https://github.com/node.png","language":"Perl","readme":"\n################################################################\n\nCircos - flexible and automatable circular data visualization\n\nMartin Krzywinski\nCanada's Michael Smith Genome Sciences Center\nBritish Columbia Cancer Agency\n\nmartink@bcgsc.ca\nwww.circos.ca\n\n################################################################\n\n0. INTRODUCTION\n   0.a   what is circos?\n   0.b   requirements\n\n1. GETTING STARTED\n   1.a   installation \n   1.b   executing scripts\n   1.c   testing GD\n   1.d   tools\n   1.e   batch files\n   1.f   configuration files\n\n2. BUGS\n   2.a \t report bugs and comments\n   2.b   known issues\n\n3. INSTALLATION PROBLEMS\n   3.a   missing modules\n\n4. OTHER ISSUES\n   4.a   configuration paths\n   4.b   typical errors and how to fix them\n   4.b.1 numerical parameter units\n\n################################################################\n\n0. INTRODUCTION\n\n0.a  What is circos?\n\nCircos is a program for the generation of publication-quality,\ncircularly composited renditions of genomic data and related\nannotations.\n\nCircos is particularly suited for visualizing alignments, conservation\nand intra and inter-chromosomal relationships.\n\nBut wait. Also, Circos is useful to visualize any type of information\nthat benefits from a circular layout. Thus, although it has been\ndesigned for the field of genomics, it is sufficiently flexible to be\nused in other data domains.\n\n0.b  Requirements\n\nPerl 5.8.x, or newer, is highly recommended. In addition to the core\nmodules that come with your Perl distribution, some CPAN modules are required.\n\nOn UNIX systems, for a list of modules required by Circos, run\n\n\u003e cd bin\n\u003e ./list.modules\n\nOn UNIX systems, to test whether you have these modules, run\n\n\u003e cd bin\n\u003e ./test.modules\n\nCircos supports TTF fonts. A few fonts are included in fonts/.\n\nUNIX users likely do not need to install perl on their systems, since it is commonly included by default. Windows users on the other hand usually do not have Perl and need to install it - Strawberry Perl or ActiveState Perl.\n\n  http://strawberryperl.com\n  http://www.activestate.com/activeperl\n\nBoth Windows Perl distributions have their own module manager that make it easy to install, update and remove modules.\n\n\n1. GETTING STARTED\n\nRefer to online tutorials for installation, configuration and troubleshooting\n\n  http://www.circos.ca/documentation/tutorials/configuration/\n\n1.a  Installation\n\nOn UNIX systems, use 'tar' to extract the files.\n\n\u003e tar xvfz circos-x.xx.tgz\n\u003e cd circos-x.xx\n\nOn Windows, use an archiver like WinZip or WinRAR or Window's built-in\nsupport for Zip files.\n\nYou don't need to move or edit any files in the main distribution.\n\n1.b  Executing Scripts\n\nCircos is written in Perl, which is an interpreted language. This\nmeans that the program files are plain-text and are passed through the\nPerl interpreter in order to run.\n\nOn UNIX systems, to run the scripts you simply need to make sure that\nthe files are executable (they should be already)\n\n\u003e chmod +x bin/circos\n\nafter which you can execute them directly\n\n\u003e bin/circos \n\nThe association between the bin/circos script and perl is created by\nthe first line in the script]\n\n#!/bin/env perl\n\nwhich instructs the shell to run the perl binary and provide the\nscript as input. See notes on /bin/env below.\n\nOn Windows, you'll also want to work from the command line (DOS\nwindow), but you'll need to call perl explicitly. Once you've\ninstalled a Perl distribution, like Strawberry Perl or ActiveState\nPerl, you should be able to run the interpreter which has been placed\nin your PATH by the installation process.\n\nC:\u003eperl -V\n...information about version of perl\n\nTo run Circos, \n\nC:\u003eperl C:\\path\\to\\circos\\bin\\circos [any command-line parameters]\n\nAnytime you see instruction to run a script, such as\n\n\u003e tools/bin/binlinks ...\n\nsubstitute instead\n\nC:\u003eperl tools\\bin\\binlinks ...\n\nAlso note that on UNIX file paths use \"/\" as a separation\n(e.g. /bin/env) and on Windows \"\\\" is used (e.g. C:\\perl\\bin\\perl).\n\n1.c  Testing GD\n\nTo test your GD installation to make sure your Perl distribution can\ncreate graphics and handle True Type fonts.\n\n\u003e bin/gddiag\n\nLook at the created gddiag.png. It should look like this\n\n  http://www.circos.ca/documentation/tutorials/configuration/png_output/images\n\nIf you don't see any text, see 4.b.2 below.\n\nIf you get an error like\n\n-bash: /bin/env: No such file or directory\n\nthen your 'env' binary is likely in /usr/bin (e.g. on Mac OS X) Check this by \n\n\u003e which env\n/usr/bin/env\n\nTo fix this, either change the first line in scripts in bin/* and tools/*/bin to \n\n#!/usr/bin/env perl\n\nor make a symlink from /usr/bin/env to /bin/env\n\n\u003e sudo su\n\u003e cd /bin\n\u003e ln -s /usr/bin/env env\n\nNow try creating the example image\n\n\u003e cd circos-x.xx\n\u003e cd example\n\u003e ../bin/circos -conf etc/circos.conf\n\nTo get some verbose reporting about file I/O , use \n\n\u003e ../bin/circos -conf etc/circos.conf -debug_group io,summary\n\nPlease see L\u003chttp://www.circos.ca\u003e for documentation. There are a\nlarge number of tutorials that described how the configuration files\nare formatted. Tutorials need to be downloaded separately.\n\n1.d  Tools\n\nThere are several helper scripts, available separately, that are designed\nto aid you in processing your data.\n\nMany of these involve manipulating link files. These tools independent\nscripts and are covered in Tutorial 9.\n\n  http://www.circos.ca/documentation/tutorials/utilities\n\nThe tools can be downloaded independently. Note that the stand-alone\ntools distribution may contain scripts that are newer than those\nbundled with Circos. To check this, look at the release date for the\narchives at L\u003chttp://www.circos.ca/software/download\u003e.\n\n1.e Batch Files\n\nThere may be batch files scattered throughout the data/ and tutorial/\ndirectories. These files begin with\n\n#!/bin/bash\n\nand are designed for use in UNIX environments.\n\n1.f Configuration files\n\nCentral configuration files with global parameters are found in\netc/. See etc/README for details about the contents of this file and\nhow the \u003c\u003cinclude\u003e\u003e directive is used to link them.\n\nFor a full explanation of the configuration system, see\n\n  http://www.circos.ca/documentation/tutorials/configuration/configuration_files\n\n\n2. BUGS\n\n2.a  Report bugs and comments\n\nI appreciate any and all comments you may have about Circos. Please\nuse the Google Group for questions and bug reports.\n\n  http://groups.google.com/group/circos-data-visualization\n\n2.b  Known issues\n\nGD does not draw rotated text correctly when the font size is small\nfor certain fonts. For example, using a font size of 6pt, text drawn\nan an angle is drawn with letters upright. If you see this, increase\nthe font size of the text.\n\nFonts with which this problem occurs are\n\n  CMUBright-Roman\n  CMUTypewriter-Regular\n\nFor this reason, TTF versions of these fonts are used, rather than OTF.\n\n3. INSTALLATION PROBLEMS\n\n3.a  Missing modules\n\n  http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules/\n\nIn order to run Circos you may need to install some modules from CPAN\n(www.cpan.org). You will need the modules listed at L\u003chttp://www.circos.ca/software/requirements\u003e.\n\nIf you run Circos and get a message like\n\nCan't locate Config/General.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux\n-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-mu\nlti /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl\n/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_\nperl .) at ./bin/circos line 121.\n\nthen you do not have a module installed. It may be that you have the module elsewhere,\nbut Perl cannot find it. In this case, the error message is barking at the fact that\nConfig::General is not installed.\n\nYou can install the module using CPAN (if CPAN module is installed)\n\n\u003e perl -MCPAN -e shell\n% install Config::General\n\nMake sure that you are using the same perl binary to install the module as for Circos.\n\nAlternatively, you can grab the module from CPAN directly. Use search.cpan.org to find\nthe module.\n\n\u003e wget http://search.cpan.org/~tlinden/Config-General-2.31/General.pm\n\u003e tar xvfz Config-General-x.xx.tgz\n\u003e cd Config-General-x.xx.tgz\n\u003e perl Makefile.PL ; make ; make test\n\u003e make install\n\nIf you are getting 'permission denied' errors during installation of\nthe module, then you're likely attempting to write into your system's\ndefault Perl install, and don't have permission to do so. To fix this,\nrepeat the module installation as root (administrator).\n\n\u003e sudo su\n\u003e perl -MCPAN -e shell\n...\n\n\n4. OTHER ISSUES\n\n4.a  Configuration paths\n\nIf you look inside one of the configuration files you'll find\nthat it includes other configuration files using \u003c\u003cinclude\u003e\u003e and\nmakes relative mention of data files, such as\n\n  file = data/5/segdup.txt\n\nCircos tries to find the file regardless where you are running the binary from, but \nmay still run into trouble finding files specified using a relative path.\n\nTo avoid problems, run circos from its distribution directory\n\n\u003e cd circos-x.xxx\n\u003e bin/circos -conf ...\n\nAlternative, change all the paths in the .conf file to absolute paths. For example, from\n\n  \u003c\u003cinclude etc/colors.conf\u003e\u003e\n\nto\n\n  \u003c\u003cinclude /path/to/your/install/circos-x.xx/etc/colors.conf\u003e\u003e\n\nFor details about the configuration files, see etc/README and\n\n  http://www.circos.ca/documentation/tutorials/configuration/configuration_files\n\n4.b  Typical errors and how to fix them\n\n4.b.1 Dealing with errors\n\n  http://www.circos.ca/documentation/tutorials/configuration/errors\n\n4.b.2 No text in figures\n\nIf Circos is creating images, but without any text (ideogram labels,\ntick labels, etc), it is almost certain that your GD Perl module was\ncompiled without True Type support.\n\nSee the note about gddiag above.\n\nThis may be due to the fact that you don't have the True Type library\non your system (freetype), or a configuration error during GD\ninstallation.\n\nYou'll need to reinstall GD.\n\n  http://search.cpan.org/dist/GD/\n\nThis issue comes up a lot. Circos has this to say about it\n\ncircos -fake font,ttf\n\nand many threads about it have been created on the message boards\n\n  http://groups.google.com/group/circos-data-visualization/browse_thread/thread/c893b8b612c2c5cf\n\n\nREADME HISTORY\n\n2013 Feb 12 - standardized URLs for /documentation/tutorials\n\n2012 Feb 20 - added link to thread about TTF support and a command to fake TTF font error\n\n2012 Feb 5 - modified note on errors, added reference to external tutorials\n\n2011 Jul 25 - split Circos, tutorials and tools into separate archives\n\n2011 Jun 04 - started keeping track of history\n\n2011 Jul 07 - updated links to ciros.ca\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnode%2Fcircos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnode%2Fcircos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnode%2Fcircos/lists"}