Update MitoZ 3.4 to 3.5

Question

[manaswiniparija3]

I have already installed MitoZ 3.4 in a ubuntu system. I want to update the version to 3.5. Is there a way to update it without uninstalling it?

Answer 1

[Darked89]

conda create -n mitoz_35
conda activate mitoz_35
conda install -c bioconda mitoz

EDIT you can also use Singularity container: https://depot.galaxyproject.org/singularity/mitoz%3A3.5--pypl5321hdfd78af_0

[Ram]

While this installs a conda environment with mitoz 3.5, it does not technically update the existing installation. Please note that this (i.e., using conda environments) is the preferred method of using software unless you're absolutely sure you want the software globally updated to a specific version. Often, we need different versions of the same software product installed for different projects.

[Darked89]

Well, the author asked for "update without uninstall", so I assumed he/she wants to keep the 3.4 version for the time being.

[Ram]

Right, that is one interpretation. Another is that they wish to replace the existing version and not add a new version, as most users new to *nix don't understand that there's no "(un)installation" in *nix.

Answer 2

[linzhi2013]

I also prefer the method by @Darked89, which clearly shows the version of the software by its environment name.

conda create -n mitoz_36
conda install python=3.8 mitoz=3.6 # it is better to specify the version you would like to install
conda activate mitoz_36

Please note that there is a bug in MitoZ 3.5, which leads to the missing annotation of tRNA genes. Therefore, now MitoZ has been upgraded to 3.6. I did more thoughtful tests this time (but limited to Linux platforms). Please check https://github.com/linzhi2013/MitoZ for more details.

Cheers Guanliang