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MitoZ 3.2
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@linzhi2013 linzhi2013 released this 10 May 18:03
· 152 commits to master since this release
3.2
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Learn about vigilant mode.

Installation

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba create -n mitozEnv -c bioconda mitoz=3.2
$ source activate mitozEnv   # or use "mamba" or "conda" instead of "source" the command here.

$ circos --modules # check if all Perl modules required by circos are installed. Some modules could still be missing (don't know why conda did not fix them automatically). Similar problems can be seen at https://github.com/bioconda/bioconda-recipes/issues/9830

# Now we are ready to go:
$ mitoz # all subcommands are within this command now!

$ mitoz-tools # some useful tools for mitochondrial genome analysis

If the above installation method does not work for you, you can try

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba env create -n mitozEnv  -f mitozEnv.yaml
$ conda activate mitozEnv
$ pip install ./mitoz-3.2.tar.gz
# or 
$ tar -zxvf mitoz-3.2.tar.gz
$ cd mitoz-3.2
$ python3 setup.py install

Changelog

  1. Fixed a bug in 'filter_taxonomy_by_CDS_annotation.py', which did not parse the genetic code to the command correctly (always parsed 5 for all input genetic codes).

  2. '--requiring_taxa' becomes a necessary option, in case the users set '--clade Chordata' but forget to set this option (because its default was 'Arthropoda').

  3. Now the 'overlapping' information is copied to the resulting folder automatically.

  4. The circularity information now is parsed to the annotation module correctly.

  5. The length of sequence ids now is checked before running annotation.

  6. Seems that the problem which in some cases circos not drawing SVG/PNG files is fixed.

  7. For the dependency package 'ete3', now we change it to v3.1.2, this should fix the NCBITaxa() problem when creating or updating the database.

  8. The circos' problem of missing Perl modules should be fixed now if you install MitoZ via bioconda channel, please raise an issue if the problem is still there.

Don't forget to have a look at https://github.com/linzhi2013/MitoZ/wiki.

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