Build against more recent htslib versions

[jdblischak]

Migrated request from @nextgenusfs in TileDB-Inc/TileDB-VCF#455 (comment)

Summary:

• tiledb-vcf-feedstock builds libtiledbvcf against the htslib in the tiledb channel (tiledb::htslib for linux/osx and tiledb::m2w64-htslib for win)
• The tiledb channel provides htslib 1.16 and m2w64-htslib 1.15.1. The bioconda channel provides htslib 1.19
• Using the latest samtools/bcftools requires htslib 1.19
• Even though the libtiledbvcf recipe indicates htslib >= 1.15, due to the run exports of htslib recipe, the runtime requirement is very strict, eg htslib >=1.16,<1.17.0a0 on linux/osx

Proposed solution:

• Bump htslib-feedstock to 1.19
• Update m2w64-htslib-build to build and release m2w64-htslib 1.19 1.16
• Bump m2w64-htslib-feedstock to 1.19 1.16
• Bump build number in tiledb-vcf-feedstock to rebuild libtiledbvcf against more recent htslib

Blockers:

• We can't upload new htslib conda binaries to anaconda.org until the authentication token is fixed Authentication token has expired htslib-feedstock#12

[jdblischak]

tiledb::htslib 1.19 is now available for linux-64, osx-64, and osx-arm64

https://anaconda.org/tiledb/htslib/files?version=1.19

[jdblischak]

tiledb::m2w64-htslib 1.16 is now available for win-64

https://anaconda.org/tiledb/m2w64-htslib/files?version=1.16

[jdblischak]

m2w64-htslib 1.16 will be the latest we can provide for Windows builds for the time being. See TileDB-Inc/m2w64-htslib-build#4 for details

[jdblischak]

@nextgenusfs are you using linux or macOS? We recently build TileDB-VCF 0.27.1 for linux-only, which linked against the new htslib 1.19 I built, so this now solves:

mamba create --dry-run -n myenv --override-channels \
  -c conda-forge -c bioconda -c tiledb \
  "libtiledbvcf>=0.26.6" "tiledbvcf-py>=0.26.6" samtools=1.19 bcftools=1.19
## + libdeflate                        1.19  hd590300_0            conda-forge     Cached
## + openssl                          3.2.0  hd590300_1            conda-forge     Cached
## + tiledb                          2.18.3  hc1131af_1            conda-forge     Cached
## + htslib                            1.19  h81da01d_0            bioconda           3MB
## + bcftools                          1.19  h8b25389_0            bioconda         970kB
## + samtools                          1.19  h50ea8bc_0            bioconda         463kB
## + python                         3.10.13  hd12c33a_1_cpython    conda-forge     Cached
## + libtiledbvcf                    0.27.1  hb3db9ce_1            tiledb             1MB
## + tiledbvcf-py                    0.27.1  py310hde7a117_1       tiledb             2MB

[nextgenusfs]

Linux! Thanks for the efforts, I will give it a try on Monday!

[jdblischak]

In #107, I also backported this to TileDB-VCF 0.26.7 which is built against TileDB 2.17. This also rebuilt binaries against newer htslib versions for osx-64, osx-arm64, and win-64

mamba create --dry-run -n myenv --override-channels \
  -c conda-forge -c bioconda -c tiledb \
  "libtiledbvcf==0.26.7" "tiledbvcf-py==0.26.7" samtools=1.19 bcftools=1.19
## + libdeflate                  1.19  hd590300_0            conda-forge     Cached
## + openssl                    3.2.0  hd590300_1            conda-forge     Cached
## + tiledb                    2.17.4  h8c794c1_0            conda-forge        6MB
## + htslib                      1.19  h81da01d_0            bioconda           3MB
## + bcftools                    1.19  h8b25389_0            bioconda         970kB
## + samtools                    1.19  h50ea8bc_0            bioconda         463kB
## + python                   3.10.13  hd12c33a_1_cpython    conda-forge     Cached
## + libtiledbvcf              0.26.7  hb3db9ce_1            tiledb             1MB
## + tiledbvcf-py              0.26.7  py310h284cd70_1       tiledb             2MB

[jdblischak]

@nextgenusfs please let us know if you still have any trouble using TileDB-VCF with the latest samtools, etc.

[jdblischak]

Update: I was also able to build m2w64-htslib 1.19 for Windows. Future versions of TileDB-VCF will be built against this newer version. If anyone needs an older version of TileDB-VCF built against m2w64-htslib 1.19, please open a new Issue to request it

[nextgenusfs]

@jdblischak was working for me last week. Had to build a fresh conda environment due to python version but it solved successfully, thanks for the help!