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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Welcome bcbio 1.2.9 #3592

Open naumenko-sa opened 2 years ago

naumenko-sa commented 2 years ago

Hello everyone!

bcbio1.2.9 is out - thanks everyone who contributed to testing and bug fixing during the last month!

We were lucky enough to catch openssl1.1.1 > 3.0 upgrade (Sept 2021) which is pushed by many conda-forge packages. In the result, the envs which were solving ok with bcbio1.2.8 and 1.2.9a (based on 1.2.8 recipe) won't solve in 1.2.9. This issue was fixed by pinning openssl in the bioconda recipe: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bcbio-nextgen/meta.yaml#L43

Due to the large reorganization of conda environments (https://github.com/bcbio/bcbio-nextgen/issues/3538), direct updates 1.2.8 -> 1.2.9 are not possible. Install 1.2.9 with --nodata instead, and link genomes from 1.2.8. Note that snpeff is updated to 5.0 (https://github.com/bcbio/bcbio-nextgen/issues/3570), the snpeff databases should be upgraded after bcbio installation, for example, bcbio_nextgen.py upgrade -u skip --genomes hg38 will alter contents of genomes/Hsapiens/hg38/snpeff.

Let us know if you see any issues with 1.2.9!

Happy Holidays and Happy 2022!

Sergey

lbeltrame commented 2 years ago

Due to the large reorganization of conda environments, direct updates 1.2.8 -> 1.2.9 are not possible.

Actually, it is possible, although with loads of manual fiddling. Source: I was able to after trying to upgrade before this issue was posted. Took several hours and lots of effort, though.