Cutadapt installation issues

Question

[Naresh D J]

Hi,

I have installed the cutadapt on a server machine with out any errors. But when I use it results in the following error

bash: cutadapt: command not found

I am new to the linux OS and working on the servers. Can any one help me?

Thank you,
Naresh D J

[GouthamAtla]

Can u post commands how did u install cutadapt? The better way is pip install cutadapt or sudo pip install cutadapt.

[igor]

If you don't have root privileges, run:

pip install --user cutadapt

[Naresh D J]

Hi Goutham Atla,

Thank you for the reply,

I am installing it on the server machine. I do not have root access.

I have downloaded the cutadapt-1.8.3.tar.gz and installed using the command

$ python setup.py install --prefix=$USERAPPL/my_cutadapt

It produced the following.

[GouthamAtla]

I think you need to export PYTHONPATH as well. I would suggest you to run sudo pip install cutadapt. If you do not have sudo permissions, get python distributions like Anaconda, which makes life easier.

[Matt Shirley]

get python distributions like Anaconda, which makes life easier.

What? Anaconda has nothing to do user permissions. If you're suggesting that using "conda" instead of "pip" will help, then I think you're also off-base as conda's cutadapt release (1.3) is way behind the PyPI release (1.8.3). Also, please, please never recommend that anyone mess with their PYTHONPATH environment variable - especially users that seem to be having basic packaging/installation issues. PYTHONPATH should point to the system python library and the one in our $HOME/.local directory, and unless you have some extremely good reasons to change it please don't.

[GouthamAtla]

I mean to say adding to Pythonpath not entirely changing the pythonpath.

[Matt Shirley]

Sorry, I think you caught me on a grumpy day...

[Matt Shirley]

Also for future questions like this I would post in the cutadapt issue tracker.

Answer 1

[cruckert8]

You have to either specify the full path to the executable e.g.

/home/your_username/.local/bin/cutadapt

or add the directory where you installed cutadapt to your path by adding the following line to the .bashrc file in your home directory:

export PATH=$PATH:/path/to/your/cutadapt-installation

You can view your current path settings by typing:

echo $PATH

Regards,
Christian

[Naresh D J]

Hi Christian,

Thank you for the reply.

I tried like this

export PATH=$PATH:/homeappl/home/njayavel/appl_taito/my_cutadapt/bin

Is this correct way of doing it? Then I am getting this error.

 Traceback (most recent call last):
  File "/homeappl/home/njayavel/appl_taito/my_cutadapt/bin/cutadapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
ImportError: No module named cutadapt.scripts

Best Regards,
Naresh D J

[Matt Shirley]

I would take igor's advice and use the --user installation scheme. What this does is place the cutadapt module in your $HOME/.local directory and the cutadapt script in $HOME/.local/bin. What you've done so far will require that you append /homeappl/home/njayavel/appl_taito/my_cutadapt/ to your PYTHONPATH variable, but frankly I think that's a poor idea.

[zhulijuanchb]

That is the solution, one more to do is source .bashrc file thank you!