I am trying to run pggb with docker. I have followed the instruction to build the image locally. Initially I couldn't get the program to run (either with the test data or my data). After commenting set -eo pipefail in the pggb script, I figured out that wfmash was raising an error which was forcing the pipeline to stop when reaching the alignment phase. The error is both raised when using the local or pre-built containers.
wfmash: error while loading shared libraries: libwfa2cpp.so.0: cannot open shared object file: No such file or directory
Command exited with non-zero status 127
In spite of the error, it keeps going but the PAF file produced is empty. I'm tempted to install libwfa2cpp on my local cluster, but I think it would defeat the purpose of the container.
clemgoub
commented
12 months ago
Dear pggb team,
I am trying to run pggb with docker. I have followed the instruction to build the image locally. Initially I couldn't get the program to run (either with the test data or my data). After commenting
set -eo pipefailin the pggb script, I figured out thatwfmashwas raising an error which was forcing the pipeline to stop when reaching the alignment phase. The error is both raised when using the local or pre-built containers.In spite of the error, it keeps going but the PAF file produced is empty. I'm tempted to install libwfa2cpp on my local cluster, but I think it would defeat the purpose of the container.
I'm eager to hear your suggestions,
Thanks a lot,
Clément