Question: Cutadapt installation issues
0
gravatar for Naresh D J
2.8 years ago by
Naresh D J50
Turku/BTK
Naresh D J50 wrote:

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

 

rna-seq • 5.7k views
ADD COMMENTlink modified 2.8 years ago by Matt Shirley8.4k • written 2.8 years ago by Naresh D J50

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

 

ADD REPLYlink written 2.8 years ago by Naresh D J50

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.

ADD REPLYlink written 2.8 years ago by Matt Shirley8.4k

Can u post commands how did u install cutadapt ?  The better way is 

pip install cutadapt or sudo pip install cutadapt.
ADD REPLYlink written 2.8 years ago by geek_y8.6k
1

If you don't have root privileges, run:

pip install --user cutadapt
ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by igor6.2k

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.

.....................................................

running install
running build
running build_py
running build_ext
running build_scripts
running install_lib
creating /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64
creating /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6
creating /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages
creating /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/seqio.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/compat.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/align.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/_seqio.so -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/adapters.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/_qualtrim.so -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/modifiers.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/__main__.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
creating /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/scripts
copying build/lib.linux-x86_64-2.6/cutadapt/scripts/__init__.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/scripts
copying build/lib.linux-x86_64-2.6/cutadapt/scripts/cutadapt.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/scripts
copying build/lib.linux-x86_64-2.6/cutadapt/report.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/qualtrim.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/_align.so -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/colorspace.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/__init__.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/xopen.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
copying build/lib.linux-x86_64-2.6/cutadapt/filters.py -> /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/seqio.py to seqio.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/compat.py to compat.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/align.py to align.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/adapters.py to adapters.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/modifiers.py to modifiers.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/__main__.py to __main__.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/scripts/__init__.py to __init__.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/scripts/cutadapt.py to cutadapt.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/report.py to report.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/qualtrim.py to qualtrim.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/colorspace.py to colorspace.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/__init__.py to __init__.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/xopen.py to xopen.pyc
byte-compiling /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt/filters.py to filters.pyc
running install_scripts
creating /homeappl/home/njayavel/appl_taito/my_cutadapt/bin
copying build/scripts-2.6/cutadapt -> /homeappl/home/njayavel/appl_taito/my_cutadapt/bin
changing mode of /homeappl/home/njayavel/appl_taito/my_cutadapt/bin/cutadapt to 755
running install_egg_info
Writing /homeappl/home/njayavel/appl_taito/my_cutadapt/lib64/python2.6/site-packages/cutadapt-1.8.3-py2.6.egg-info

 

..................................................

 

ADD REPLYlink written 2.8 years ago by Naresh D J50

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.

ADD REPLYlink written 2.8 years ago by geek_y8.6k

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.

ADD REPLYlink written 2.8 years ago by Matt Shirley8.4k

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

ADD REPLYlink written 2.8 years ago by geek_y8.6k

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

ADD REPLYlink written 2.8 years ago by Matt Shirley8.4k

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

ADD REPLYlink written 2.8 years ago by Matt Shirley8.4k
1
gravatar for cruckert8
2.8 years ago by
cruckert810
Germany
cruckert810 wrote:

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

ADD COMMENTlink written 2.8 years ago by cruckert810

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

ADD REPLYlink written 9 months ago by zhulijuanchb0
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