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Quickstart
This is a short introductory guide for CoCoPyE. You should be able to install and run CoCoPyE within minutes, but it doesn't cover all details.
The easiest way to install CoCoPyE is by installing it as a Conda package. If you haven't used Conda before I suggest to have a look at this installation guide (I would recommend the miniconda installation as it contains less packages that you most likey won't need, but this is up to you).
Important
Please note that the Conda installation currently does not work for MacOS with ARM CPU. If you're running such a system (or do not want to use Conda for installation) you can instead follow the steps on the Installation wiki page.
Create a new environment and install CoCoPyE from the conda-forge channel:
conda create -n cocopye -c conda-forge cocopye
Activate the environment and you are ready to continue:
conda activate cocopye
Note
CoCoPyE has a low-memory option which is recommended for systems with 16GB or less RAM. See System requirements for more information.
CoCoPyE relies on UProC for protein translation and ORF detection. If you have used Conda for installation it should have been installed already as a dependency. Furthermore, both CoCoPyE and UProC require some kind of database. Both UProC (if necessary) and the databases can be downloaded automatically by executing cocopye setup download-dependencies.
After finishing the downloads you can execute cocopye setup testrun. If this runs successfully, CoCoPyE is ready to use.
The most basic command to execute CoCoPyE is
cocopye run -i <path to folder with FASTA files> -o <outfile in csv format (will be created by CoCoPyE)>
You can specify a different file extension for your FASTA files by using the --file-extension parameter (default: fna). See Usage for more information on command line arguments. You can also execute cocopye run -h or have a look at Configuration.