search

quinlan-lab / vcf2db

create a gemini-compatible database from a VCF
MIT License
55 stars 13 forks source link

Snappy import/compile failure #37

Closed Phillip-a-richmond closed 6 years ago

Phillip-a-richmond commented 6 years ago

THIS IS NOT AN ISSUE THAT NEEDS RESOLVING

I had an issue with the newest version of conda, where the python-snappy library doesn't compile correctly when you use the channel listed in the README for snappy importing.

conda install -c nlesc python-snappy=0.5

Traceback (most recent call last): File "./vcf2db.py", line 10, in import snappy File "/home/richmonp/TOOLS/anaconda/lib/python2.7/site-packages/snappy.py", line 45, in from _snappy import CompressError, CompressedLengthError, \ ImportError: /home/richmonp/TOOLS/anaconda/lib/python2.7/site-packages/../../libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/richmonp/TOOLS/anaconda/lib/python2.7/site-packages/../../libsnappy.so.1)

A simple fix is to import a different python-snappy conda install -c conda-forge python-snappy

I don't know if other users had this problem but I thought I would post what worked for my setup here.

Cheers, Phil