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gaow / omics-bma

A machinery to interrogate genomics / transcriptomics data using Bayesian Model Averaging
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eqtbma_bf GSL exception #1

Open gaow opened 8 years ago

gaow commented 8 years ago

This command fails 

eqtlbma_bf --geno list_genotypes.txt --scoord snp_coords.bed.gz --exp list_phenotypes.txt --gcoord gene_coords.bed.gz --cis 1000 --out obs_bf --outw --analys join --bfs customized   --error hybrid --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz   --priorM "prior-matrix*.txt.gz"   --gridM matrix-scalars.txt.gz -v 1 --wrtsize 3

Test data is under /home/gaow/GIT/omics-bma/src/unit-tests/data. Apparently this is a GSL exception that eqtlbma_bf failed to handle.

If --cis 5 then there is no issue. This bug should also be fixed at eqtlbma repo

gaow commented 8 years ago

I'll not fix GSL; instead I'll replace GSL's LA part with Armadillo down the line. A related issue is then how to make GSL a portable library without installing. This is possible if GSL is compiled without make install and the link dir is changed to GSL.

https://github.com/ansariazim/treeBreaker