MitoZ 3.1

Add the seqkit program to subsample clean data for mitochondrial assembly, so the users don't have to do it by themselves.

You can install MitoZ via

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba create -n mitozEnv -c bioconda mitoz=3.1
$ 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

# For me, the Perl modules "GD" and "GD::Polyline" were missing (although conda said they have been installed already when I ran 'conda install perl-gd'), I fixed them by running following three commands:
$ mamba install -c conda-forge pkg-config
$ mamba install -c anaconda gcc_linux-64
$ cpanm install GD
# I will try to fix the circos' problem in bioconda's MitoZ recipe file, but for the moment, please use the above solution, or try the "mitozEnv.yaml" solution below.
# You can use the ”cpanm“ command to install other missing Perl modules if necessary. 

# 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-3.1.tar.gz
# or 
$ tar -zxvf mitoz-3.1.tar.gz
$ cd mitoz-3.1
$ python3 setup.py install