fix cmake to find hts

[pabloaledo]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? salmon

Describe the bug Errors compiling salmon in spack with cmake

To Reproduce spack install salmon

Specifically, please provide at least the following information:

• Which version of salmon was used?: 1.10.2
• How was salmon installed (compiled, downloaded executable, through bioconda)?: through spack, that downloads source
• Which reference (e.g. transcriptome) was used?: none, the error is during compilation
• Which read files were used?: none
• Which which program options were used? RELEASE

Expected behavior Program would compile correctly

Desktop (please complete the following information):

• OS: [e.g. Ubuntu Linux, OSX]: linux x86_64
• Version [ If you are on OSX, the output of sw_vers. If you are on linux the output of uname -a and lsb_release -a]:

  Linux pablo-ThinkPad-T14-Gen-3 5.19.0-50-generic #50-Ubuntu SMP PREEMPT_DYNAMIC Mon Jul 10 18:24:29 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  No LSB modules are available.
  Distributor ID: Ubuntu
  Description:    Ubuntu 22.04.2 LTS
  Release:    22.04
  Codename:   jammy

Additional context During the update of the spack package for salmon we found hts is needed, and cmake could not find the module. We are wondering if you want/plan to use this by default.

https://github.com/spack/spack/pull/39202/commits/c3357a64a9697be4058feb555a2c4e4138793f17

[rob-p]

Hi @pabloaledo,

Thanks for the report! I am not familiar with spack. However, the bigget issue here is that I don't believe that salmon, by itself, should require/depend upon libhts. It uses libstaden for its sam/bam parsing, but that should be a self-contained dependency. We should figure out why libhts is being pulled in here.

Best, Rob

[pabloaledo]

Do you think I should redirect my question to https://github.com/jkbonfield/io_lib ?

Thanks a lot for the help !

[rob-p]

Hi Pablo,

It is probably worth checking upstream in the io_lib repo to see what the expected behavior is. I'll note that io_lib itself is not a CMake based build, so it's possible that I messed something up when creating the relevant CMake module to find libstaden. However, I believe I am correct in the assessment that the full htslib should not be necessary to build libstaden. Let's get @jkbonfield's read on this. Feel free to tag me if you open an issue in that Github repo.

--Rob