latest CAVA release is not installing gives undefined symbol error

[swatibodh]

/CAVA-1.2.3$ cava -c config.txt -i /home/swati/snpEff_latest_core/snpEff/glioma2/GRCh37/bow_gatk.vcf -o bow_gatk_cava
/home/swati/.local/bin/cava: line 4: /home/swati/.local/bin/activate: No such file or directory
Traceback (most recent call last):
File "/home/swati/.local/bin/CAVA.py", line 4, in
from cava_ import main
File "/home/swati/.local/lib/python2.7/site-packages/cava_/main.py", line 10, in
import pysam
File "/home/swati/.local/lib/python2.7/site-packages/pysam/init.py", line 1, in
from pysam.csamtools import *
ImportError: /home/swati/.local/lib/python2.7/site-packages/pysam/csamtools.so: undefined symbol: update_posmap

[vishramt7]

Hi,
I am facing the same issue on our Ubuntu20.04 server. Were you able to fix it ?
Thanks,
Vishram

[JeffreyMaurer]

I hit a similar error when running get_refmeta from the modtools python package when our Ubuntu server had pysam 0.7.6 and 0.7.7 for python 2.7

Running sudo easy_install pysam==0.20.0 resolved this specific issue:

from pysam.csamtools import *
ImportError: /home/USER/.local/lib/python2.7/site-packages/pysam/csamtools.so: undefined symbol: update_posmap

My assumption is that it's because it's the first "static inline" function the linker gets to and old pysams have incompatible flags? Not an expert, but it's the only function in that particular file that has "static inline" modifier.