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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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Import genomic features from the file as a GRanges object ... trying URL 'ftp://ftp.ebi.ac.uk... #83

Open horyunchung opened 3 weeks ago

horyunchung commented 3 weeks ago

When importing salmon quant.sf files, tximeta tries to build the matching TxDb with txdbmaker package. It tries to download the annotation gtf file from ebi

Import genomic features from the file as a GRanges object ... trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/gencode.v46.annotation.gtf.gz'

That fails on my machine because I am sitting behind a firewall that does not allow ftp traffic. Is there any compelling reason why the URL is given as 'ftp://'? To get it working I changed the entry in the file hashtable.csv in extdata/ from "ftp://" to "https://" which works.

Best

Ho

mikelove commented 3 weeks ago

Hi Ho!

I can make a switch for https. I'll do that today and it can be released in a few weeks.

Mike

mikelove commented 3 weeks ago

Can you try from github:

devtools::install_github("thelovelab/tximeta")
txi <- tximeta(..., skipFtp=TRUE)