Question: Issue about install Cutadapt in ubuntu1404
0
gravatar for Joe
10 months ago by
Joe30
USA
Joe30 wrote:

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"

cutadapt • 432 views
ADD COMMENTlink written 10 months ago by Joe30
1

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

ADD REPLYlink written 10 months ago by Santosh Anand3.4k

Thank you so much! Problem solved!!!!

ADD REPLYlink written 10 months ago by Joe30
1

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.

ADD REPLYlink written 10 months ago by genomax42k

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!

ADD REPLYlink written 10 months ago by Joe30

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)

ADD REPLYlink written 10 months ago by WouterDeCoster25k
2

@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.

ADD REPLYlink written 10 months ago by Santosh Anand3.4k

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.

ADD REPLYlink written 10 months ago by WouterDeCoster25k

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

ADD REPLYlink written 10 months ago by Santosh Anand3.4k
2

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

ADD REPLYlink written 10 months ago by genomax42k

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

ADD REPLYlink written 10 months ago by Santosh Anand3.4k
1

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

ADD REPLYlink written 10 months ago by WouterDeCoster25k

Thanks I will try to figure out by myself.

ADD REPLYlink written 10 months ago by Joe30
1

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

ADD REPLYlink written 10 months ago by h.mon11k
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