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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
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ImportError: libhts.so.2 #153

Closed yaskermezli closed 3 years ago

yaskermezli commented 3 years ago

Hi,

I'm getting this error after installation of gtftk on cluster :

Traceback (most recent call last): File "/home/kermezly/anaconda3/envs/pygtftk/bin/gtftk", line 27, in from pygtftk.cmd_manager import CmdManager File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk/cmd_manager.py", line 27, in from pygtftk.arg_formatter import ArgFormatter File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk/arg_formatter.py", line 14, in import pybedtools File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pybedtools/init.py", line 12, in from . import contrib File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pybedtools/contrib/init.py", line 3, in from . import venn_maker File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pybedtools/contrib/venn_maker.py", line 12, in from pybedtools import helpers File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pybedtools/helpers.py", line 13, in import pysam File "/home/kermezly/anaconda3/envs/pygtftk/lib/python3.6/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * ImportError: libhts.so.2: cannot open shared object file: No such file or directory

dputhier commented 3 years ago

Hi Yasmina, It seems that this error is related to pysam (which is not a direct dependency of pygtftk but is probably required by pybedtools). Did you installed pygtftk using bioconda ? Otherwise you could also try a 'pip install pysam'.

Maybe you could try a 'pip install pysam'

dputhier commented 3 years ago

Or better:

 pip install pysam -U
yaskermezli commented 3 years ago

Yes! Solved Thank you.

xinwei-sher commented 2 years ago

Worked on me! Thanks.