installation error

[AnneJRomero]

I have installed jitterbug and I have the conda environment with the required dependencies:

psutil 5.7.0 py27hdf8410d_1 conda-forge
pybedtools 0.8.1 py27h4bd9754_2 bioconda
pysam 0.16.0.1 py27ha863e18_1 bioconda
python 2.7.15 h5a48372_1011_cpython conda-forge

but when testing it out I get the following error:
(TE27) [ar14g12@cyan51 jitterbug]$ jitterbug.py ../bam_files/D_L2_sort.bam ../TE_annotation/TE_anno.gff3
Traceback (most recent call last):
File "./jitterbug.py", line 21, in
from Run_TE_ID_reseq import *
File "/mainfs/scratch/ar14g12/PhD/tomato/TE/jitterbug/jitterbug/Run_TE_ID_reseq.py", line 6, in
import pysam
File "/home/ar14g12/.local/lib/python2.7/site-packages/pysam/init.py", line 5, in
from pysam.libchtslib import *
ImportError: /home/ar14g12/.local/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: PyUnicodeUCS2_DecodeUTF8

Googling the error it looks like there is a mismatch between the python installation and the package, one being encoded in unicodeUSC2 and the other in USC4.
https://stackoverflow.com/questions/11878666/python-undefined-symbol-pyunicodeucs2-decodeutf8

Do you have a quick fix for this problem?

[hanshanmengqi]

Hi @AnneJRomero,

I think it's probably because of the version of dependencies.
In my case, I downloaded the dependencies as shown below:

matplotlib 2.2.5
matplotlib-base 2.2.5
matplotlib-venn 0.11.5
memory-profiler 0.41
numpy 1.15.4
pandas 0.24.2
pybedtools 0.7.10
pysam 0.8.4
python 2.7.15
setuptools 44.0.0

Hope it's helpful.

Han