installation of deep tools on mac using anaconda

[Pranidhi Sood]

Hi — I am trying to install the latest version of deeptools using anaconda, but keep getting a segmentation fault error 11 when I run most of the tools.

These are the versions of the dependencies I have. Do you have any idea why this might be happening?

numpy 1.12.1
scipy 0.19.1
py2bit 0.2.1
pybigwig 0.3.5
pysam 0.11.2.2
matplotlib 2.1.0
python 3.6.3

For example when I run bamCoverage -b file.bam -o tmp.bw I get “Segmentation fault: 11”.
Although when I run plotPCA -h , I get a help menu.
When I run nosetests --with-doctest --ignore-files=plotCoverage deep tools I get a Seg fault 11, too.

Any advice?
Thanks,
Pranidhi


Pranidhi Sood, Ph.D.
Post-doctoral Fellow, Marshall Lab
Department of Biochemistry & Biophysics
UCSF Mission Bay
600 16th St.
San Francisco, CA 94143-2200

[Pranidhi Sood]

Also — deeptools is version 2.5.3.

Thanks!

Pranidhi Sood, Ph.D.
Post-doctoral Fellow, Marshall Lab
Department of Biochemistry & Biophysics
UCSF Mission Bay
600 16th St. 
San Francisco, CA 94143-2200

[Devon Ryan]

What happens if you run:

python -c “import pyBigWig”

That shouldn’t cause an issue, but perhaps something went weird during the build. 

Sent from my iPhone

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[Björn Grüning]

Hi Pranidhi,

can you send me the log from the conda installation?
I suspect we need to pin pysam.

Thanks,
Bjoern

[Pranidhi Sood]

Hi Bjorn and all — I ended up having success installing it with the anaconda python 2.7… I was using 3.6 initially… 

Thank you so much for your fast response, though! I really appreciate it…

Pranidhi

[Bart Rymen]

Hi I encountered a similar problem after having updated my mac to mac os sierra 10.13.1. Before deep tools was running fine. Now I also get for most tools "segmentation fault error 11".

Is there another solution then reinstalling the app under python 2.7?

Best regards,

Bart

[Devon Ryan]

If you're using python 3.5.4, then please run "conda install -c
conda-forge python=3.5.4". For some reason the copy of that exact
version of python in the default channel is problematic.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany