x811zou / beastie Goto Github PK

Takes around 1.5 hours on real data from what I have seen. The issue is that the LDmatrix calls take a long time.

I opened an issue upstream to potentially help address: CBIIT/nci-webtools-dceg-linkage#159

BEASTIE/annotation.py tries to run Rscript --vanilla annotate_LD_new.R, but if beastie is installed it looks in the current working directory rather than the directory annotate.py is actually in.

A workaround is to copy all the .R files from the install directory to the current directory, but that's not ideal.

Command and error

# /usr/local/bin/iBEASTIE2
/usr/local/bin/iBEASTIE2: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/bin/iBEASTIE2)

I fixed a few issues to uncover this one, you can check out a dirty version of the changes in my fork here: https://github.com/zackgomez/BEASTIE

On the first run of the iBEASTIE2 executable libtbb2 was missing which was an easy fix. This issue with glibc looks to be due to building iBEASTIE2 in a different docker environment based on gcc:11. The running environment is ubuntu:20.10.

My guess is the best solution is to build the executable in an ubuntu:20.10 environment as well, but think @tncowart might know more as the original author of the Dockerfile.