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I tried installing pip3 install deeptoolsintervals the error is:

 deeptoolsintervals/tree/tree.c:1:20: fatal error: Python.h: No such file or directory
    compilation terminated.
    error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1

I have Ubuntu 16.04.7 and Python versions installed:

ls /usr/bin | grep python

dh_python2
dh_python3
python
python2
python2.7
python2.7-config
python2-config
python3
python3.5
python3.5m
python3.9
python3m
python-config
x86_64-linux-gnu-python2.7-config
x86_64-linux-gnu-python-config

I have installed deeptools under python3.9

$ git clone https://github.com/deeptools/deepTools
$ cd deepTools
$ python3.9 setup.py install
Tomerikoo
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xyz0o
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    Does this answer your question? [fatal error: Python.h: No such file or directory](https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory) – bereal Mar 09 '21 at 12:18
  • I tried `sudo apt-get install python3-dev`, but it sets it up on python3.5 and when I run `pip3 install deeptoolsintervals`, I have the same error – xyz0o Mar 09 '21 at 12:41

1 Answers1

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the problem was that I was not using the same version of python each time, so I installed the python-env for python3.9

sudo apt-get install python3.9-dev

and then

pip3.9 install deeptoolsintervals

successfully installed.

xyz0o
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