Answers.Body: <p>The simplest solution is to install conda/Anaconda</p>
  <p>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:</p>
  <pre><code>conda install -c bioconda circos 
  conda install -c bioconda/label/broken circos 
  conda install -c bioconda/label/cf201901 circos 
  </code></pre>
  <p>This is a preferred solution because the <code>make</code> 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: <a href="https://docs.anaconda.com/anaconda/install/windows/" rel="nofollow noreferrer">https://docs.anaconda.com/anaconda/install/windows/</a></p>
  <p>You could install <code>brew</code> but this would be a bit messy,</p>
  <pre><code>/bin/bash -c &quot;$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)&quot;
  </code></pre>
  <p>because you would be using a perl environment within a simulator.</p>
  <p>The alternative is to do what @user324810 and install <code>make</code> explicitly and is described here,
  <a href="https://stackoverflow.com/questions/23293589/perl-module-install-error-cpan">https://stackoverflow.com/questions/23293589/perl-module-install-error-cpan</a></p>
  <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-16T11:05:33.607Z
Answers.Text: 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.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-16T11:13:40.367Z
Answers.Text: 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
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-16T11:43:38.857Z
Answers.Text: 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.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-29T15:55:31.083Z
Answers.Text: "*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.
Answers.UserDisplayName: merv
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-29T20:03:28.657Z
Answers.Text: Good point @merv, (in fairness I did say start at the top), and its certainly a safer recommendation. If its not entirely mirrored, the entire package should be removed IMO . If you have information in this regard on this package it would be good to share it here. Environments are strongly recommended, 100% agreed, but its the first dive into Anaconda it can a lot to take and the OP may not go with the suggestion (I don't think they did) - its just a suggestion after all.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-29T20:51:17.963Z
Answers.Text: "*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](http://bioconda.github.io/user/install.html#set-up-channels).
Answers.UserDisplayName: merv
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-29T22:41:47.483Z
Answers.Text: Not quite what I meant but thanks @merv I like the docs. Anaconda is too cool and too useful not to be full part of any longer and these are useful.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-15T10:06:11.370Z
Answers.LastActivityDate: 2022-03-15T10:06:11.370Z
Answers.UserDisplayName: M__
Body: <p>Im trying to install the missing modules of Circos without success.</p>
  <p>The error code is:</p>
  <pre><code>cpan[1]&gt; 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 &quot;make&quot;: 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
  </code></pre>
  <p>I'm running Ubuntu in Windows and already tried in another computer</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-16T11:07:00.553Z
Comments.Text: 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?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-14T14:06:51.487Z
Comments.Text: @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...
Comments.UserDisplayName: Matteo Ferla
Tags: <perl><molecular-genetics><circos>
Title: Installing modules in perl for Circos
ThreadText: # Installing modules in perl for Circos
  
  (Asked by: username_0 on 2022-03-15)
  
  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
  
  **Tags:** perl, molecular-genetics, circos
  
  > **Comments:**
  > **username_1**: 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?  
  > **username_2**: @username_3'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...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-03-15. Score: 1
  
  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.
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_3**: 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  
  > **username_3**: 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.  
  > **username_4**: "*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.  
  > **username_3**: Good point @username_4, (in fairness I did say start at the top), and its certainly a safer recommendation. If its not entirely mirrored, the entire package should be removed IMO . If you have information in this regard on this package it would be good to share it here. Environments are strongly recommended, 100% agreed, but its the first dive into Anaconda it can a lot to take and the OP may not go with the suggestion (I don't think they did) - its just a suggestion after all.  
  > **username_4**: "*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](http://bioconda.github.io/user/install.html#set-up-channels).  
  > **username_3**: Not quite what I meant but thanks @username_4 I like the docs. Anaconda is too cool and too useful not to be full part of any longer and these are useful.  
  
  ---
  
  