lslochov
commented
5 years ago Hi @taylorjtamu , are you using the master branch or the dev branch of SVE? The dev branch has a number of fixes that the master branch doesn't have, which may work out better.
Alternatively, you could use the Docker or Singularity image of SVE, which packages all the applications and dependencies and allows you to bypass direct compilation, and does have locked versions of the dependencies. I can provide these to you, if you like.
The 0.1.0 release package is missing all files for multiple dependencies in the src directory, which causes it to completely fail to build. Dependencies with folders but no files present that trigger errors and failures during build: htslib speedseq bcftools
I was able to clone htslib from the git repository and get past its failure case.
Due to issues in the speedseq repository similar to what I reported in https://github.com/TheJacksonLaboratory/SVE/issues/25 I am unable to clone that repository in. I had a copy of that repository from an earlier (a few months back) attempt to build SVE when the repository was still whole and slotting that one in did get past this failure case.
bcftools fails as it's also empty. At this point I stopped trying to use the release as it's clear it's missing too many files.
I was hoping that the release would have a locked version of the various dependencies so that I could avoid some of the issues I'm seeing and have reported with getting the software to compile cause by dead links to dependencies.
An updated, functioning release would be appreciated.