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RahmanTeam / CAVA

CAVA (Clinical Annotation of VAriants)
MIT License
14 stars 9 forks source link

latest CAVA release is not installing gives undefined symbol error #13

Open swatibodh opened 4 years ago

swatibodh commented 4 years ago

/CAVA-1.2.3$ cava -c config.txt -i /home/swati/snpEff_latest_core/snpEff/glioma2/GRCh37/bow_gatk.vcf -o bow_gatkcava /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 commented 2 years ago

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

JeffreyMaurer commented 1 year ago

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.