I know this is might be a silly question, but I am wondering how it is possible to install cutadapt in a user defined directory like, for instance, /home/Tools/Cutadapt/.
Thank you in advance for the feedbacks.
In my opinion the easiest would be to just install cutadapt using bioconda and then symlink to that user-defined directory, but it's unclear why you would want to do so.
This also doesn't seem to be a pure bioinformatics question, which might be more suitable for StackOverflow.
I wanted to give the same answer.
pip install --user --upgrade cutadapt
sudo ln -s ~/.local/bin/cutadapt [your location]
Thank you for your answers. I am trying to find a way for having available multiple versions of cutadapt, for reproducibility issues.
Then you need virtual environments. Which you can make with conda.
conda create -n myenv cutadapt=1.13
source activate myenv
Thank you for your reply. I was wondering whether there might be any strategy alternative to venv.....
I'd like to explore possible python-independent solutions
It's a python package, so unless you want to use docker or singularity you're not going to have much luck with a python-independent solution.
Bash Environment Modules, although Python virtual environments are extremely useful, so I'd consider your choices carefully.
At least I use environment modules in conjunction with venvs and conda, so you can module load instead of source activate. I don't see these are necessarily separate solutions.
I don't really see why you would like to do that, but good luck.
Doesn't really add to the topic, but I recently saw that cutadapt is now multithreaded, but only on Python3, so you may consider to install it directly under Py3 using a virtual environment as WouterDeCoster suggested.
This is really a good point. Thank you !
Cutadapt has minimal dependencies so with Python 3, you could also do the
following assuming the python3-venv module is installed:
# install latest version
python3 -m venv cutadapt
pip install cutadapt
# install version 1.14
python3 -m venv cutadapt14
pip install cutadapt==1.14
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