Error in cutadapt installation

Question

[nivya.james2016]

Hi all,

I am trying to install cutadapt in ububtu 14.04.4 LTS. I am unable to install due to SSL errors. Here i am attaching the error commands generated. Could anyone help me in installing this tool?

$ sudo pip install cutadapt 
Downloading/unpacking cutadapt 
Cleaning up... 
Exception: 
Traceback (most recent call last): 
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 122, in main 
    status = self.run(options, args) 
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 278, in run 
    requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) 
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1198, in prepare_files 
    do_download, 
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1376, in unpack_url 
    self.session, 
  File "/usr/lib/python2.7/dist-packages/pip/download.py", line 546, in unpack_http_url 
    resp = session.get(target_url, stream=True) 
  File "/usr/share/python-wheels/requests-2.2.1-py2.py3-none-any.whl/requests/sessions.py", line 467, in get 
    return self.request('GET', url, **kwargs) 
  File "/usr/lib/python2.7/dist-packages/pip/download.py", line 237, in request 
    return super(PipSession, self).request(method, url, *args, **kwargs) 
  File "/usr/share/python-wheels/requests-2.2.1-py2.py3-none-any.whl/requests/sessions.py", line 455, in request 
    resp = self.send(prep, **send_kwargs) 
  File "/usr/share/python-wheels/requests-2.2.1-py2.py3-none-any.whl/requests/sessions.py", line 558, in send 
    r = adapter.send(request, **kwargs) 
  File "/usr/share/python-wheels/requests-2.2.1-py2.py3-none-any.whl/requests/adapters.py", line 385, in send 
    raise SSLError(e) 
SSLError: [Errno 1] _ssl.c:510: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed 

Storing debug log for failure in /home/shanthi/.pip/pip.logenter code here

Appreciate your help.

Thank you

Answer 1

[Jeffin Rockey]

Would be easier through conda.

Download and run https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh if 64 bit.

Then exit and re-login for ~/.bashrc entries to take effect or run source ~/.bashrc instead.

Then install cut adapt with command conda install -c bioconda cutadapt

(You would not need sudo privileges for doing any of the above.)

[nivya.james2016]

I was able to download and install cutadapt using this method. Thank you so much.

Answer 2

[gb]

Did you try:

sudo pip install --user --upgrade cutadapt

[nivya.james2016]

Yes i tried but the same error as above was coming.

Answer 3

[dariober]

See if this Q&A on stack overlflow helps https://stackoverflow.com/questions/25981703/pip-install-fails-with-connection-error-ssl-certificate-verify-failed-certi

According to the top answer you may just need to add flags --trusted-host pypi.org --trusted-host files.pythonhosted.org to your pip command.

(Not that I particularly recommend trying random things found in random posts...)

[nivya.james2016]

I tried adding flags but was of no avail.