How to compile with conda?

[Hoeze]

Hi, could you please provide some information how to compile this package within a conda-environment?
I guess I have to somehow build libtiledb with cmake -DFORCE_EXTERNAL_HTSLIB=OFF?

[ihnorton]

Hi @Hoeze, are you able to build with these steps?: https://docs.tiledb.com/developer/tiledbvcf/installation/python

We will add support for building against libtiledb and htslib from conda (see #48) -- in order to facilitate making a conda package too. However, I need to update the package for compatibility with arrow changes (some tests currently fail) -- will do as soon as possible.

[Hoeze]

Hi @ihnorton, thanks for your answer.

Using your instructions did not work because I was missing some header files in conda (where do I get header files for e.g. zlib?).
Compiling against the system is not possible for the same reason.

Yesterday I was able to compile against conda's htslib:

1. first compile libtiledbvcf using cmake -DFORCE_EXTERNAL_HTSLIB=OFF <libtiledbvcf_folder> && make
2. python setup.py install the python package.
   However, I did not test it yet, I only tried the import.

[ihnorton]

Hi @Hoeze, as soon as the next arrow release is available, I will submit a conda recipe for this package -- the release process is happening now. TileDB-VCF has some test failures when building against arrow 0.15, and these are fixed upstream in the upcoming arrow 0.16. (I haven't been able to find a workaround for this issue on our side yet, so I'm going to defer to the imminent release for a fix).

[Hoeze]

Thanks a lot @ihnorton!

[ihnorton]

Hi @Hoeze, sorry about the delay here. I've uploaded an initial conda package for linux.

• package: https://anaconda.org/tiledb/tiledbvcf-py
• you can see the build recipe: https://github.com/TileDB-Inc/staged-recipes/tree/tiledb/tiledb-vcf
• install with:
  conda install -c conda-forge -c bioconda -c tiledb tiledbvcf-py

If you want to build in your own environment w/ tiledb and htslib installed, use python setup.py install --libtiledbvcf=${CONDA_PREFIX} (see #59).

I will work on submitting this to bioconda soon, that seems like a better channel than conda-forge due to the scope and htslib dependency.

[ihnorton]

@aaronwolen was this fixed by #98?

[aaronwolen]

Actually, no. I just tried following the python install directions inside a fresh ubuntu container and it went belly up linking the aws sdk. It's some kind of issue w/ conda because the CLI builds fine w/ conda deactivated.

I'll investigate but let me know if you have any suggestions, @ihnorton.

[gspowley]

Closing this issue since it has been inactive. Please reopen if there is still an issue.