Cutadapt installation problem

Question

[e.antoun]

Hi,

I am attempting to install the latest version of cutadapt (1.9) using the source code. I have downloaded cutadapt-1.9.tar.gz, extracted it and ran the following:

python setup.py install --user

Cutadapt install fine, but then when I check the version, it says I have installed version 1.3. I then try the following:

pip install --user --upgrade cutadapt

to see if it will upgrade the program, but it does nothing and I still only have version 1.3 installed.

Can anyone help m with how to get the latest version of cutadapt? I am running python 2.7 so it should work fine.

Thanks

Answer 1

[dariober]

Make sure version 1.3 doesn't come before 1.9 in your PATH. Look at the output of 'which cutadapt' and 'echo $PATH'

[e.antoun]

Thanks for the reply.

The output of which cutadapt is: /local/software/python/2.7.5/bin/cutadapt

and echo $PATH gives:

/local/software/python/2.7.5/bin/:/usr/lib64/qt-3.3/bin:/local/software/moab/default/sbin:/local/software/moab/default/bin:/local/software/torque/default/sbin:/local/software/torque/default/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin

From that, neither version is in my PATH. So would I need to put 1.9 into my PATH for it to work?

Answer 2

[e.antoun]

Problem solved, I needed to put my locally installed cutadapt version into my PATH, as the older version was installed on the system that I don't have admin access to.