Comments (5)
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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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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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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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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Glad you got it set up and thank you so much for posting the solutions!
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Related Issues (20)
- Add test for npvector
- Split docs into separate pages HOT 1
- installation error HOT 10
- how to prepare the a special bed fild for Higlass HOT 1
- mean +/- error HOT 1
- 'Invalid line' message when aggregating bed file HOT 3
- Set up error HOT 2
- aggregate bedgraph keeps being killed HOT 5
- obsolete "clodius aggregate bigwig" example on the main page HOT 1
- Ability to support file-like objects in `clodius.tiles` HOT 1
- Unable to convert bed to States Data (multivec) file using clodius bedfile-to-multivec HOT 11
- cooler >0.9.0 support HOT 7
- Pandas FutureWarning: Series.__getitem__ deprecation warning HOT 2
- tiff -> mrmatrix?
- Split documentation into smaller chunks
- bigwig_test.py fails with "numpy.ufunc size changed" HOT 1
- turn on test_bedarcsdb_tiles1?
- Clodius aggregate with new assembly HOT 3
- Clodius aggregate with custom assembly: TypeError: Can't broadcast HOT 3
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