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Question: Cutadapt installation - user defined directory
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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.

ADD COMMENTlink 19 months ago davide.chiarugi • 20
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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.

ADD REPLYlink 19 months ago
WouterDeCoster
39k
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I wanted to give the same answer.

pip install --user --upgrade cutadapt
sudo ln -s ~/.local/bin/cutadapt [your location]
ADD REPLYlink 19 months ago
gb
• 780
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Thank you for your answers. I am trying to find a way for having available multiple versions of cutadapt, for reproducibility issues.

ADD REPLYlink 19 months ago
davide.chiarugi
• 20
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Then you need virtual environments. Which you can make with conda.

E.g.:

conda create -n myenv cutadapt=1.13
source activate myenv
ADD REPLYlink 19 months ago
WouterDeCoster
39k
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Thank you for your reply. I was wondering whether there might be any strategy alternative to venv.....

ADD REPLYlink 19 months ago
davide.chiarugi
• 20
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Why?

ADD REPLYlink 19 months ago
WouterDeCoster
39k
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I'd like to explore possible python-independent solutions

ADD REPLYlink 19 months ago
davide.chiarugi
• 20
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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.

ADD REPLYlink 19 months ago
Devon Ryan
90k
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Bash Environment Modules, although Python virtual environments are extremely useful, so I'd consider your choices carefully.

ADD REPLYlink 19 months ago
andrew.j.skelton73
5.7k
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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.

ADD REPLYlink 19 months ago
Devon Ryan
90k
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I don't really see why you would like to do that, but good luck.

ADD REPLYlink 19 months ago
WouterDeCoster
39k
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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.

ADD REPLYlink 19 months ago
ATpoint
17k
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This is really a good point. Thank you !

ADD REPLYlink 19 months ago
davide.chiarugi
• 20
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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
ADD REPLYlink 19 months ago
Vimalkumar Velayudhan
• 190

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