Issue about install Cutadapt in ubuntu1404

Question

[Joe]

Hi, I try to install cutadapt 0.9.5 in my ubuntu 14.04

I download the tar.gz file and type:

matt@matt-Inspiron-3847:~/Installs/cutadapt-0.9.5$ python setup.py install --user

The result I get is shown in below link. https://github.com/Jinggg2016/NGS/issues/2

Then I type : matt@matt-Inspiron-3847:~/Installs/cutadapt-0.9.5$ cutadapt cutadapt: command not found

I did sudo apt-get install python-dev, then type "cutadapt", still show "cutadapt: command not found"

[Santosh Anand]

try running /home/matt/.local/bin/cutadapt

[Joe]

Thank you so much! Problem solved!!!!

[GenoMax]

You need to append the directory where cutadapt was installed to your $PATH.

Do export PATH=/home/matt/.local/bin:$PATH and then try cutadapt.

[Joe]

Hi, It works, but only temporary, if I close the terminal and open a new terminal, it will still show "cutadapt: command not found ". I need to do the command line you suggest again to make "cutadapt" work.

Do you have solution to make it permanent?

Thanks!

[WouterDeCoster]

You would benefit a lot from learning more about the linux environment :-) This is a pretty basic problem.
In this case, you would need to change the $PATH in .bashrc or .bash_profile (not sure which one is more recommended)

[Santosh Anand]

@Walter I would say .bash_profile. see http://stackoverflow.com/questions/415403/whats-the-difference-between-bashrc-bash-profile-and-environment

The ~/.bash_profile would be used once, at login. The ~/.bashrc script is read every time a shell is started. This is analogous to /.cshrc for C Shell.

One consequence is that stuff in ~/.bashrc should be as lightweight (minimal) as possible to reduce the overhead when starting a non-login shell.

[WouterDeCoster]

Thanks for clearing that up! (Guess I should check how messed up those files in my system are by now)

@Walter

Ah well, close enough.

[Santosh Anand]

Errrrrrr... Sorry for the typo Wouter. My head is going crazy with a presentation due tomorrow, and I'm not able to detach myself from biostars. Grrrrrrrrrrr

[GenoMax]

Want your account suspended for today, just say so :)

[Santosh Anand]

Hahaha. I didn't see that coming :) Not for this time, but it's becoming a serious issue now!

[WouterDeCoster]

Haha no problem, and good luck with that presentation :-p

[Joe]

Thanks I will try to figure out by myself.

[h.mon]

Why such an old version? cutadapt 0.95 dates from July 2011. Current version is 1.13, released some days ago.