search

Bioconductor / AnnotationHub

Client for the Bioconductor AnnotationHub web resource
15 stars 12 forks source link

fixed windows specific BamFile loading error #7

Closed FelixErnst closed 5 years ago

FelixErnst commented 5 years ago

Tested on Windows and Linux using BioC 3.9/R 3.6

FelixErnst commented 5 years ago

should fix the problems surfacing here:

https://github.com/Bioconductor/Contributions/issues/1106

mtmorgan commented 5 years ago

The plan is instead to allow Rsamtools to read index files without '.bai' extensions, which is done in https://github.com/Bioconductor/Rsamtools/commit/f76b367f979ba4e7e2121034112994b06d7cd577 (will be v. 2.1.1 in devel; when that builds without problem it'll be ported to release). The AnnotationHub recipe should be modified to simply read the index file as downloaded.

FelixErnst commented 5 years ago

thanks for the fix. so this will hit the SPB probably tomorrow. Is there a plan for the update of AnnotationHub?

lshep commented 5 years ago

There is a major bug in the devel version of the hubs that I'm working on now... once that is fixed and once the Rsamtools propagates I will fix the AnnotatinoHub recipe ...

FelixErnst commented 5 years ago

Thanks for the info.