search

aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
MIT License
10 stars 9 forks source link

LD_LIBRARY_PATH problems #49

Open aryarm opened 5 years ago

aryarm commented 5 years ago

We try to automatically install WASP for those who don't have it, but

  1. The conda envs must have LD_LIBRARY_PATH set inside them. Otherwise, snp2h5 won't work
  2. Also, if the user is manually installing dependencies, you shouldn't assume that their HDF5 libraries are in the conda directory (or indeed, that conda even exists on their machine). Instead, specify this as an optional config option.
aryarm commented 4 years ago

this should be resolved by this issue

aryarm commented 3 years ago

just a note here that conda v4.9 supports specifying env variables in a yaml file!

so that could be an alternative solution to this problem. Although, I'm not sure whether we can append/prepend to env variables rather than overriding them