I tried to upgrade perl, but circos doesn't work anymore!

[Johnathan Bouchard]

Hi! 

I have Circos 0-67.1 installed. I used it the last time about 4 months ago, and it was working great. I tried to use again today, and I got the following error:

you are missing one or more Perl modules, require newer versio523 installed modules have no parsable version number

(use 'o conf show_unparsable_versions 1' to show them)ns, or some modules failed to load. Use CPAN to install it as described ....

Since I had already installed everything in the past, I simply used "CPAN upgrade" and got the following error message during installation:

523 installed modules have no parsable version number

(use 'o conf show_unparsable_versions 1' to show them)

I tried to run circos and got the following errors:

missing Params::Validate

  error Can't locate Params/Validate.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 37) line 1.

missing Math::Round

  error Can't locate Math/Round.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 32) line 1.

missing Font::TTF::Font

  error Can't locate Font/TTF/Font.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 21) line 1.

missing Clone

  error Can't locate Clone.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 6) line 1.

missing List::MoreUtils

  error Can't locate List/MoreUtils.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 26) line 1.

missing Config::General

  error Can't locate Config/General.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 7) line 1.

missing GD

  error Can't locate GD.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 22) line 1.

missing SVG

  error Can't locate SVG.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 44) line 1.

missing Math::Bezier

  error Can't locate Math/Bezier.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 29) line 1.

missing Readonly

  error Can't locate Readonly.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 39) line 1.

missing GD::Polyline

  error Can't locate GD/Polyline.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 23) line 1.

missing Math::VecStat

  error Can't locate Math/VecStat.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 33) line 1.

missing Set::IntSpan

  error Can't locate Set/IntSpan.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 41) line 1.

missing Statistics::Basic

  error Can't locate Statistics/Basic.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 42) line 1.

missing Regexp::Common

  error Can't locate Regexp/Common.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 40) line 1.

missing Text::Format

  error Can't locate Text/Format.pm in @INC (@INC contains: /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin/../lib /Users/johnathan_bouchard/Applications/circos-0.67-1/bin /Users/johnathan_bouchard/src/bioperl-1.2.3 /Users/johnathan_bouchard/src/ensembl/modules /Users/johnathan_bouchard/src/ensembl-compara/modules /Users/johnathan_bouchard/src/ensembl-variation/modules /Users/johnathan_bouchard/src/ensembl-funcgen/modules /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at (eval 48) line 1.

I am pretty sure that it is a path problem, but I am not sure. I am using a Mac. I would greatly appreciate any suggestion! Thank you!

[Martin Krzywinski]

If you upgraded Perl, you'll need to reinstall the modules.

Different versions of Perl do not share modules.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Johnathan Bouchard]

Hi Martin,

Thank you very much for your help! I am learning how to use the Unix system and path variable. According to the documentation, Circos uses the path variable to determine where perl is. I have just used perlbrew to install a new perl installation (i.e. 5.20.2), which should have all the modules, no? When I type, "which perl", I get /opt/local/bin/perl. This is the path Circos looks atl right? This is my .bash_profile file

PATH="$PATH:/Users/johnathan_bouchard/Documents/vcftools/bin"

PATH="$PATH:/Users/johnathan_bouchard/Documents/tabix"

PATH="$PATH:/Users/johnathan_bouchard/Applications/bedtools2/bin"

export PERL5LI=B/Users/johnathan_bouchard/Documents/vcftools/perl

export CLICOLOR=1

export LSCOLORS=gxfxcxdxbxegedabagacad

export TERM=xterm-color

export PS1="\[\e[36;1m\]\u@\[\e[32;1m\]\w> \[\e[0m\]"

alias ls='ls -G'

alias ll='ls -hl'

source ~/perl5/perlbrew/etc/bashrc

PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-1.2.3

PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules

PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules

PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules

PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-funcgen/modules

export PERL5LIB

export PATH=/usr/local/bin:$PATH

export PATH=/usr/local/bin:$PATH

##

# Your previous /Users/johnathan_bouchard/.bash_profile file was backed up as /Users/johnathan_bouchard/.bash_profile.macports-saved_2014-12-27_at_19:16:40

##

# MacPorts Installer addition on 2014-12-27_at_19:16:40: adding an appropriate PATH variable for use with MacPorts.

export PATH="/opt/local/bin:/opt/local/sbin:$PATH"

# Finished adapting your PATH environment variable for use with MacPorts.

# added by Anaconda 2.1.0 installer

export PATH="/Users/johnathan_bouchard/anaconda/bin:$PATH"

export LC_ALL=en_US.UTF-8

export LANG=en_US.UTF-8

#personal scripts

PATH="$PATH:/Users/johnathan_bouchard/bin"

#path to perlbrew perl version

PATH="$PATH:/Users/johnathan_bouchard/perl5/perlbrew/perls/perl-5.20.2/bin"

Hence, when I log in, this is my $PATH:

-bash: /Users/johnathan_bouchard/anaconda/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/local/bin:/Users/johnathan_bouchard/perl5/perlbrew/bin:/Users/johnathan_bouchard/perl5/perlbrew/perls/5.19.11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin:/Users/johnathan_bouchard/Documents/vcftools/bin:/Users/johnathan_bouchard/Documents/tabix:/Users/johnathan_bouchard/Applications/bedtools2/bin:/Users/johnathan_bouchard/bin:/Users/johnathan_bouchard/perl5/perlbrew/perls/perl-5.20.2/bin: No such file or directory

I think that I should remove some paths in my.bash_profile so Circos can find the new perl installation to see if I am missing modules. Are there some lines that I could delete in my. bash_profile file to resolve this issue? Once Circos refers to the correct perl version, then I can verify if all required modules are present. Thank you very much for your time! I have generated several figures for my thesis that need some corrections (that I am trying to do by running Circos).

Johnathan

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[Martin Krzywinski]

No environment variables are required for Circos to run.

As long as the upgraded perl binary is in your path, so that

> which perl

points to it, you're fine.

Circos automatically uses the perl binary that is in your path using the 

> /bin/env perl

directive

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Johnathan Bouchard]

Hi Martin,

So. I could simply copy-and-paste the binaries from perl 5.20.2 into the regular path?

Thank you!

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