Question: Error in cutadapt installation
0
gravatar for nivya.james2016
8 months ago by
nivya.james20160 wrote:

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

cutadapt • 381 views
ADD COMMENTlink modified 8 months ago by dariober10k • written 8 months ago by nivya.james20160
2
gravatar for Jeffin Rockey
8 months ago by
Jeffin Rockey1.1k
Karimannoor
Jeffin Rockey1.1k wrote:

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.)

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jeffin Rockey1.1k

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

ADD REPLYlink written 8 months ago by nivya.james20160
0
gravatar for gb
8 months ago by
gb780
gb780 wrote:

Did you try:

sudo pip install --user --upgrade cutadapt
ADD COMMENTlink written 8 months ago by gb780

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

ADD REPLYlink written 8 months ago by nivya.james20160
0
gravatar for dariober
8 months ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:

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...)

ADD COMMENTlink written 8 months ago by dariober10k

I tried adding flags but was of no avail.

ADD REPLYlink written 8 months ago by nivya.james20160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1014 users visited in the last hour