The new Ensembl marts for release 95 are now live on www.ensembl.org.
If you are using biomaRt, you can change your host to access our most recent data:
ensemblmart95 <- useEnsembl(biomart=“ensembl")
When a new version of ensembl is release, Bioconductor generates annotation resources to provide to our users through our annotationhub based on the new version. I've done this many times for many versions. It appears there is some difficulty generating the resources based on the latest ensembl 95. From what I can tell my scripts are getting stuck when the site is expecting an authentication username and password. I'm not sure if this is triggered by a certain number of website hits from the same IP address or an issue with the new data? Is there any way around this as it hasn't been an issue in the past? I've traced it in the code that goes and accesses the gtf for each species ftp://ftp.ensembl.org/pub/release-95/gtf/ and when I put in a check to which species it failed on, when I try to access that directory if brings up an authentication box. The species that it fails on changes per run and is not always the same. I also sent an email to the firstname.lastname@example.org .
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