Question: Trouble with danpos2 installation - can anyone help?
1
gravatar for a.rex
4 months ago by
a.rex180
a.rex180 wrote:

I have used conda to install both R and rpy2. When I try to run python danpos.py -h to install the danpos package I get the following error:

Traceback (most recent call last):
  File "danpos.py", line 6, in <module>
    from functions import danpos
  File "/path/danpos-2.2.2/functions.py", line 4, in <module>
    from wigs import Wigs
  File "/path/danpos-2.2.2/wigs.py", line 3, in <module>
    from wig import Wig
  File "/path/danpos-2.2.2/wig.py", line 4, in <module>
    from rpy2.robjects import r,FloatVector
  File "/usr/local/lib/python2.7/dist-packages/rpy2/robjects/__init__.py", line 16, in <module>
    import rpy2.rinterface as rinterface
  File "/usr/local/lib/python2.7/dist-packages/rpy2/rinterface/__init__.py", line 92, in <module>
    from rpy2.rinterface._rinterface import (baseenv,
ImportError: No module named _rinterface

Is this an issue with the R installation path? How can I resolve this. Thank you!

danpos python installation • 266 views
ADD COMMENTlink modified 4 months ago by h.mon24k • written 4 months ago by a.rex180
1

You can install danpos with conda.

ADD REPLYlink written 4 months ago by h.mon24k

Nope, this doesn't work

ADD REPLYlink written 4 months ago by a.rex180
2

And would you mind telling us "how" that doesn't work? Error message? We are notoriously bad at reading your mind.

ADD REPLYlink written 4 months ago by WouterDeCoster37k

This was the error when using the conda link above. PackagesNotFoundError: The following packages are not available from current channels:

  • danpos
  • samtools
ADD REPLYlink modified 4 months ago • written 4 months ago by a.rex180

Make sure your channels are correctly configured for bioconda.

ADD REPLYlink written 4 months ago by WouterDeCoster37k
1
gravatar for h.mon
4 months ago by
h.mon24k
Brazil
h.mon24k wrote:

I just installed it:

source $HOME/bin/miniconda3/bin/activate
conda create -n DANPOS2-2.2.2
conda activate DANPOS2-2.2.2
conda install -c imperial-college-research-computing danpos
danpos.py -h
danpos version 2.2.2
For help information for each function, try:
python danpos.py <function> -h

Functions:
        dpos:
                analyze each protein-binding position (~100
                to ~200bp wide) across the whole genome,
                e.g. nucleosome positions.
  
ADD COMMENTlink written 4 months ago by h.mon24k
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