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Im trying to install the missing modules of Circos without success.

The error code is:

cpan[1]> install Config::General
Reading '/home/asg28/.cpan/Metadata'
  Database was generated on Mon, 14 Mar 2022 03:29:03 GMT
Running install for module 'Config::General'
Fetching with HTTP::Tiny:
http://www.cpan.org/authors/id/T/TL/TLINDEN/Config-General-2.63.tar.gz
Fetching with HTTP::Tiny:
http://www.cpan.org/authors/id/T/TL/TLINDEN/CHECKSUMS
Checksum for /home/asg28/.cpan/sources/authors/id/T/TL/TLINDEN/Config-General-2.63.tar.gz ok
Scanning cache /home/asg28/.cpan/build for sizes
............................................................................DONE
'YAML' not installed, will not store persistent state
Configuring T/TL/TLINDEN/Config-General-2.63.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Config::General
Writing MYMETA.yml and MYMETA.json
  TLINDEN/Config-General-2.63.tar.gz
  /usr/bin/perl Makefile.PL INSTALLDIRS=site -- OK
Running make for T/TL/TLINDEN/Config-General-2.63.tar.gz
Can't exec "make": No such file or directory at /usr/share/perl/5.30/CPAN/Distribution.pm line 2225.
  TLINDEN/Config-General-2.63.tar.gz
  make -- NOT OK
  No such file or directory
Failed during this command:
 TLINDEN/Config-General-2.63.tar.gz           : make NO

I'm running Ubuntu in Windows and already tried in another computer

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  • $\begingroup$ Can you install the build-essential package on WSL (Windows Subsystem for Linux)? Does sudo apt install build-essential work and, if so, does it fix your issue? $\endgroup$
    – terdon ♦
    Mar 16, 2022 at 11:07
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    $\begingroup$ @M__'s answer is perfect, but it merits saying that in the 13 years (as of 2022) since its release many other packages in R or Python can generate plots like Circos. I think Plotly calls it chord plot or something, but most call them Circos plots —like a "hoover" is any vacuum cleaner in BE. Some have less functionality but are way easier to use and install... $\endgroup$
    – Matteo Ferla
    Apr 14, 2022 at 14:06

1 Answer 1

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The simplest solution is to install conda/Anaconda

Then type any one of the following. Start with the top command and if it is unavailable go to the next commend down - only needs work once:

conda install -c bioconda circos 
conda install -c bioconda/label/broken circos 
conda install -c bioconda/label/cf201901 circos

This is a preferred solution because the make will already be configured along with any other dependency and in addition you can run it directly on Windows without an intervening simulator as described here: https://docs.anaconda.com/anaconda/install/windows/

You could install brew but this would be a bit messy,

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

because you would be using a perl environment within a simulator.

The alternative is to do what @user324810 and install make explicitly and is described here, https://stackoverflow.com/questions/23293589/perl-module-install-error-cpan

The error is easy enough but there will be future dependencies which will not be installed and a once an for all solution is a better option and diagnosing and installing each dependency in turn.

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  • $\begingroup$ The question is about Perl. Is there a conda for perl? As far as I know, conda is a python thing although their site does claim it can do other languages. $\endgroup$
    – terdon ♦
    Mar 16, 2022 at 11:05
  • $\begingroup$ Yes. Conda is not singly a Python thing, its a complete environment in this case installing independent Perl and a separate environment to prevent it interacting with system Perl. Using 'brew' is a Perl thing but particularly on Mac its nightmare. Conda is the main reason in my opinion there hasn't been an active uptake of Docker $\endgroup$
    – M__ ♦
    Mar 16, 2022 at 11:13
  • $\begingroup$ Just to add, trying is believing. Conda is very cool, because it will load up all dependencies and always works, its better than CPAN, albeit CPAN is likely buried in their somewhere. The only issue is uninstalling because the dependencies remain in place, so you really need to create a new environment for each project (which like doesn't always happen) and delete the whole thing to 'uninstall' everything. $\endgroup$
    – M__ ♦
    Mar 16, 2022 at 11:43
  • $\begingroup$ "type any one of the following" - this is not a good recommendation. While Anaconda Cloud automatically lists all labels found on package builds, no one should need the alternative labels (outside of someone deliberately reproducing a previous analysis that used one of those builds). Furthermore, Bioconda expects conda-forge to be prioritized, so a proper recommendation should be conda install -c conda-forge -c bioconda circos. Even better, create a dedicated environment. $\endgroup$
    – merv
    Mar 29, 2022 at 15:55
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    $\begingroup$ "If its not entirely mirrored" - not sure I follow what you mean. You mean my comment about needing the conda-forge channel? That's in the docs. $\endgroup$
    – merv
    Mar 29, 2022 at 20:51

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