Tutorials for Circos use in the WINDOWS7 environment

A friend of the system biology elective course to talk about the use of Circos, so on the download installation used a bit. Well, here are the questions to use and encounter, for reference only.

First, download the installation package1.strawberry Perl

Because the Circos software relies on the Perl language to compile the environment, it is not Perl by default in the Windows environment, so you need to install the Perl compilation environment before you can run Circos properly.

(1). Download Perl software address : http://www.perl.org. then select the Download menu.

(2). Go to the Download menu page, there will be three kinds of operating system download files, we choose Windows, recommended download Strawberry Perl this version.

(3). Click on the link, will jump to another download page, at this time depending on whether your machine is 32-bit or 64-bit selection to download the correct version.

(4). Run the. msi file and enter the test command in console cmd: perl-v, if the version information can be output correctly, the installation is successful.

2.Circos

(1). To access http://circos.ca/, select the Software menu.

(2). Select Sub-menu, download menu.

(3). Enter download there are more versions to choose from, and there are some ancillary software that can only select the latest version of the download. This is a compressed file, decompression can be used without the need to install.

3. Necessary Modules

To be able to run Circos, also rely on some necessary modules, here is the basic module, if you run the routine to prompt miss the Perl module * * *, you need to manually download the missing module. If the error is missing the necessary module Statistics::basic, need to download.

(1). Visit http://www.cpan.org/, enter the name of your missing module in search, and then search.

(2). Select the first search result.

(3). Download this module. This is a file to be unzipped, need to extract two times, and then we find all the. pm files in this, generally in the root directory and LIB, but there are exceptions, such as Statistics::basic This module is in the Basic folder, This is also why the Strawberry Perl CPAN console uses the GET, make, instal command to download and install the module, but the reason for the missing module is running.

(4). Place the module's. PM File in the Circos Lib folder. It is important to note that similar to the above Statistics::basic to the Lib folder now create a folder statistics, and then copy the basic. PM file into the Statistics folder. Repeat the 1-4-step operation to download the other basic modules and copy them to the Lib folder, as shown in the directory.

4. Summary

Overall, the completion of the above steps will still take a long time, walnuts posterity, so I have all the things downloaded, and then packaged, can be downloaded directly at this address: http://download.csdn.net/detail/u012321815/8658879

second, the use of Circos1. Using the self-with routines

Circos This compressed file comes with a routine project, and we can use this routine to test if we can figure it out properly.

(1). Open the console cmd and jump to our Circos root directory, as this is the root directory of circos-0.67-7. Use the CD command to jump to the root directory, depending on where you extracted it.

(2). Execute the perl command. Perl. \bin\circos-conf. \example\etc\circos.conf. This command can be understood, Perl is the command header, this is very good understanding, is to use Perl to compile execution, this command now has three parameters, the first is to use the Bin folder Circos to run the command, the second parameter is a description, refers to the compilation of conf file The last parameter is the exact location of the. conf file. We open etc This folder, you can see there are many other. conf files, these files are actually circos.conf dependencies, we can open circos.conf see there are a lot of <<include ***.conf>> statement, which can be understood as relying on this. conf file. Successfully executed, we can see the time spent from the console and generate a circos.png image in the root directory.

2. Other routines on the use of the official website

Other official website routines have been downloaded here, but the test passed several, and some still have errors, yet to learn.

(1). To access the http://circos.ca/documentation/tutorials/quick_start/, you can see that there are 9 engineering routines.

(2). Here's a third example, click the Third link. You can see that there are three menus, Lesson, image, and configuration. The first one is a simple explanation, the second is the picture that results from running the result, and the third is the configuration file, which is the core part of the code.

(3). We can simply follow the configuration of the document inside the original project based on direct modification. The configuration here requires three files: circos.conf, ideogram.conf, and ticks.conf. We copy and paste directly into the original project file (you can also re-create the folder, and then manually add the three files), and then execute. It is recommended to use Perl. \bin\circos-conf. \example\etc\circos.conf-outputdir Output-outputfile Circos.png command, this is different from the previous add a few parameters, respectively, the folder name of the output picture, here is replaced with output, the other is the name of the export file, here is replaced by Circos.png, these two can be set by themselves. The default is not set, that is, in the root directory circos.png, this will overwrite the previous routine generated pictures, so the output image should not have the same name.

3. Summary

My friend and I passed the first few routines, but there are other routines without testing or testing did not succeed, so I hope to teach you a lot!

Tutorials for Circos use in the WINDOWS7 environment