Perl version issue of MitoZ=3.4

[SongCU]

Hi @linzhi2013,

Thank you so much for your effort to update to version 3! However, there was a problem with circos when installing and using version 3.4 (GD module).

I changed the pearl version and it worked well.

So, Please update Perl version in yml file.

https://github.com/linzhi2013/MitoZ/releases/download/3.4/mitozEnv.yml

perl=5.26 ==> perl=5.32

the old version of perl makes circos GD module error!

+++ Maybe need to be install perl module "Statistics::discriptive" using conda

conda install -c bioconda perl-statistics-descriptive

name: mitozEnv channels:

• conda-forge
• bioconda
• defaults dependencies:
  • fastp
  • megahit
  • spades>=3.15.4
  • requests
  • bs4
  • libgd
  • biopython
  • blast
  • bwa
  • circos=0.69
  • ete3>=3.1.2
  • hmmer=3.1b2
  • infernal=1.1.1
  • openjdk
  • perl=5.32
  • perl-list-moreutils
  • perl-params-validate
  • perl-clone
  • perl-bioperl
  • python>=3.6
  • samtools
  • seqkit
  • tbl2asn

[linzhi2013]

Hi SongCU,

Thank you very much for the suggestion!

I would test it and see if it works for most cases (because sometimes Perl=5.2.6 worked for me, but sometimes not, even on the same machine). If it works, then I would update the method.

@other users, you are also encouraged to drop a comment here to let me know whether this method works for you or not. Thanks!

Cheers Guanliang

[paul-bio]

hi @linzhi2013 . I have struggled fighting errors from cpamn during visualizing step.

However when I installed MITOZ3 with yml.file above, it worked without any error messages! I agree that there could be a crash when using different perl version.

Anyway thanks for the wonderful program!

Best wishes. Paul.

[linzhi2013]

hi @linzhi2013 . I have struggled fighting errors from cpamn during visualizing step.

However when I installed MITOZ3 with yml.file above, it worked without any error messages! I agree that there could be a crash when using different perl version.

Anyway thanks for the wonderful program!

Best wishes. Paul.

Hi Paul,

Thanks for your comment!

When I tested Perl 5.32, I got new problems, and sometimes it is still very annoying to deal with. Therefore, I have provided the Singularity, Docker, and Conda-Pack versions of MitoZ (https://github.com/linzhi2013/MitoZ/wiki/Installation#4-conda-pack). Hope it's easier for the users to install MitoZ with them since they have packaged (almost) everything all together.

Cheers Guanliang