On Thu, Feb 8, 2018 at 11:13 AM, James Bonfield <j...@sanger.ac.uk> wrote: > On Thu, Feb 08, 2018 at 09:32:00AM -0700, Brent Pedersen wrote: >> I've been working more with crams lately and in some cases, it seems >> the default behavior of htslib is to automatically start downloading >> reference files locally even though I have not set REF_CACHE or >> REF_PATH. This is deep in a complex pipeline behind several layers of >> abstraction, but I think this is the default. > > If you don't set them it'll automatically default to using the EBI for > REF_PATH and ~/.cache/hts-seqs (IIRC) for REF_CACHE. > > If you really wish to totally disable them, keep REF_CACHE clear and > set REF_PATH to somewhere with no files, eg /foo, and it'll fail the > search. > > It should then fail. > > James > > -- > James Bonfield (j...@sanger.ac.uk) > The Sanger Institute, Hinxton, Cambs, CB10 1SA > > > -- > The Wellcome Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE.
Thanks for the reply. It seems a better solution would be to fail unless REF_CACHE or REF_PATH are set. I'm having scenarios where a user uses the wrong reference and samtools detects this and starts downloading with message: "Creating reference cache directory $HOME/.cache/hts-ref" I never want to have stuff download automatically. Even setting REF_PATH=xx , it will start downloading if I specify the wrong reference. -Brent ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
