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Nico-FR avatar Nico-FR commented on July 17, 2024

I managed to install it with python3.7 -m pip install clodius
But when I tried clodius aggregate bedfile /tmp/sample.short.bed:

Traceback (most recent call last):
  File "/home/nmary/.local/bin/clodius", line 5, in <module>
    from clodius.cli.aggregate import cli
ModuleNotFoundError: No module named 'clodius'

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pkerpedjiev avatar pkerpedjiev commented on July 17, 2024

Looks like this is the important part:

  src/pairixmodule.c:33:20: fatal error: Python.h: No such file or directory

Could you see if this helps: https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory?

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Nico-FR avatar Nico-FR commented on July 17, 2024

Indeed kg-config --cflags --libs python3 return python3.5m:

-I/usr/include/python3.5m -I/usr/include/x86_64-linux-gnu/python3.5m -lpython3.5m

while the installation procedure is looking for -fPIC -I/usr/include/python3.6m

I have python.h in python3.5m:
ls -lh /usr/include/python3.5/Python.h

-rw-r--r-- 1 root root 2.9K Oct  9 18:52 /usr/include/python3.5/Python.h

But /usr/include/python3.6m doesn't exist. I will try to find a solution tomorrow.

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Nico-FR avatar Nico-FR commented on July 17, 2024

Hi,
I solve the problem just by installing the needed version of python dev sudo apt-get install python3.6-dev.

I had another problem that I solved (I give my solution just in case):

curl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \
> ./sample.short.bed
clodius aggregate bedfile ./sample.short.bed

return:

Traceback (most recent call last):
  File "/home/nmary/.local/bin/clodius", line 5, in <module>
    from clodius.cli.aggregate import cli
  File "/home/nmary/.local/lib/python3.6/site-packages/clodius/cli/__init__.py", line 18, in <module>
    from . import (  # noqa: F401
  File "/home/nmary/.local/lib/python3.6/site-packages/clodius/cli/aggregate.py", line 23, in <module>
    import scipy.misc as sm
  File "/usr/lib/python3/dist-packages/scipy/misc/__init__.py", line 51, in <module>
    from scipy.special import comb, factorial, factorial2, factorialk
  File "/usr/lib/python3/dist-packages/scipy/special/__init__.py", line 627, in <module>
    from ._ufuncs import *
ModuleNotFoundError: No module named 'scipy.special._ufuncs'

So I removed the scipy version 0.17.0 installed by ubuntu sudo apt-get purge python3-scipy and installed the last one 1.5.4 pip3 install scipy and the aggregate command works!

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pkerpedjiev avatar pkerpedjiev commented on July 17, 2024

Glad you got it set up and thank you so much for posting the solutions!

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