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linzhi2013 / MitoZ

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
https://doi.org/10.1093/nar/gkz173
GNU General Public License v3.0
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Perl version issue of MitoZ=3.4 #152

Open SongCU opened 2 years ago

SongCU commented 2 years ago

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:

linzhi2013 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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