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BruneauLab-GladstoneInstitutes / computing-envs

Docker and Singularity files for single cell analysis
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Python.h is missing #3

Open h836472 opened 2 years ago

h836472 commented 2 years ago

Dear Developers,

"pip3 install fa2" command fails, when trying to build monocle3 using the docker file. Error message:

x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fdebug-prefix-map=/build/python3.7-dIfpci/python3.7-3.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python3.7m -c fa2/fa2util.c -o build/temp.linux-x86_64-3.7/fa2/fa2util.o fa2/fa2util.c:4:10: fatal error: Python.h: No such file or directory

include "Python.h"

            ^~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1

It looks like Python.h is not properly listed in the include section (actual location of the folder: ./home/jupyter-user/miniconda/pkgs/python-3.7.4-h265db76_1/include/python3.7m)

Can you please fix the dockerfile?

h836472 commented 2 years ago

adding

ENV CPATH=/home/jupyter-user/miniconda/pkgs/python-3.7.4-h265db76_1/include/python3.7m/

should solve this issue