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Cutadapt installation - user defined directory

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.

cutadapt installation
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written by davide.chiarugi • davide.chiarugi

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.

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written by WouterDeCoster WouterDeCoster

I wanted to give the same answer. 

pip install --user --upgrade cutadapt
sudo ln -s ~/.local/bin/cutadapt [your location]
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written by gb gb

Thank you for your answers. I am trying to find a way for having available multiple versions of cutadapt, for reproducibility issues.

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written by davide.chiarugi • davide.chiarugi

Then you need virtual environments. Which you can make with conda.

E.g.:

conda create -n myenv cutadapt=1.13
source activate myenv
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written by WouterDeCoster WouterDeCoster

Thank you for your reply. I was wondering whether there might be any strategy alternative to venv.....

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written by davide.chiarugi • davide.chiarugi

I'd like to explore possible python-independent solutions

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written by davide.chiarugi • davide.chiarugi

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.

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written by Devon Ryan Devon Ryan

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.

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written by Devon Ryan Devon Ryan

I don't really see why you would like to do that, but good luck.

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written by WouterDeCoster WouterDeCoster

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.

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written by ATpoint ATpoint

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
source cutadapt/bin/activate
pip install cutadapt
deactivate 

# install version 1.14
python3 -m venv cutadapt14
source cutadapt14/bin/activate
pip install cutadapt==1.14
deactivate
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written by vimalkvn vimalkvn

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