SOFT : MitoZ
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Site du soft: https://github.com/linzhi2013/MitoZ
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LICENSE:
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GPL-v3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/MitoZ
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Load binaries and environment:
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-> Version v3.6 (BUG with Spades. Load module bioinfo/SPAdes/3.15.5_compil after module bioinfo/MitoZ/3.6)

#Need Miniconda
module load devel/Miniconda/Miniconda3
module load bioinfo/MitoZ/3.6
module load bioinfo/SPAdes/3.15.5_compil

To unload module, unload  in order:

module unload bioinfo/MitoZ/3.6
module unload devel/Miniconda/Miniconda3

Warning! Default cpu:8 (don't forget to adjust --thread_number for mitoz  and --cpus-per-task for Slurm)

The installation of the NCBI taxonomy database for the ete3 package must be done by each user:

$ mkdir ~/work/.etetoolkit (if already exist mv ~/.etetoolkit ~/work/.etetoolkit)
$ ln -s ~/work/.etetoolkit ~/
$ module load devel/Miniconda/Miniconda3
$ module load bioinfo/MitoZ/3.6
$ module load bioinfo/SPAdes/3.15.5_compil
$ python3
>from ete3 import NCBITaxa
>ncbi = NCBITaxa()
>ncbi.update_taxonomy_database()

Example directory for use on cluster:
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/usr/local/bioinfo/src/MitoZ/example_on_cluster

To submit: sbatch test_MitoZ-v3.6.sh 

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.