Hi Paul, I am testing it and there is no problem. >>> from pygr import worldbase >>> ponAbe2 = worldbase.Bio.Seq.Genome.PONAB.ponAbe2(download=True) INFO downloader.download_unpickler: Beginning download of http://biodb.bioinformatics.ucla.edu/GENOMES/ponAbe2/ponAbe2.gz to /home/deepreds/test/ponAbe2.gz...
And, you may need to unset PYGRDATAPATH as well. Yours, Namshin Kim On Fri, Sep 4, 2009 at 10:04 AM, Paul Rigor (gmail) <paulri...@gmail.com>wrote: > Hi Namshin, It's not set, my script sets that environment variable to '., > http://biodb2.bioinformatics.ucla.edu:5000' I've made sure to remove > .pygrdata files, etc. > Thanks > Paul > > > On Thu, Sep 3, 2009 at 6:02 PM, Namshin Kim <deepr...@gmail.com> wrote: > >> Hi Paul, >> Would you please give your WORLDBASEPATH? >> >> $ echo $WORLDBASEPATH >> >> Thanks, >> Namshin Kim >> >> >> >> On Fri, Sep 4, 2009 at 9:54 AM, Paul Rigor (gmail) >> <paulri...@gmail.com>wrote: >> >>> Hi Namshin, >>> I'm still encountering the same error as before regarding the download of >>> genome resources. Download the 44way alignment also does not download the >>> necessary dependencies. Could there by something wrong with the URL paths >>> saved in on the resources. You specified 'biodb2' but during the download, >>> the url's are directed to 'biodb.' >>> >>> With WOLRDBASEPATH not set, I get the following error. >>> >>> Please see: >>> INFO downloader.download_unpickler: Beginning download of >>> http://biodb.bioinformatics.ucla.edu/GENOMES/ponAbe2/chromFa.tar.gz to >>> /extra/bal >>> dig1/genomics/pygrdata/genomes/ponAbe2.tar.gz... >>> INFO downloader.download_monitor: downloaded 8192 bytes (3593.0%)... >>> INFO downloader.download_unpickler: Download done. >>> INFO downloader.uncompress_file: untarring >>> /extra/baldig1/genomics/pygrdata/genomes/ponAbe2.tar.gz... >>> ... >>> ReadError: not a gzip file >>> >>> However, when I set my WORLDBASEPATH to use the biodb2 server, the >>> download is successful. So there's something wrong with the hardcoded url >>> that's distributed with pygr (0.8 beta). But perhaps the xmlrpc resources on >>> the server should be fixed as well. >>> >>> Thanks, >>> Paul >>> >>> >>> >>> On Thu, Sep 3, 2009 at 4:22 PM, cjlee112 <cjlee...@gmail.com> wrote: >>> >>>> >>>> Yes, please pass on to Namshin any debugging information you can supply. >>>> >>>> Thanks! >>>> >>>> Chris >>>> >>>> On Sep 3, 2009, at 3:26 PM, Paul Rigor (gmail) wrote: >>>> >>>> > Hi Chris, >>>> > >>>> > Does this mean that the 44way alignment distributed by the UCLA >>>> > server is foobar since I ran exactly those same commands and no >>>> > genome dependencies were downloaded? >>>> > >>>> > Thanks, >>>> > Paul >>>> >>>> >>> >>> >>> >>> >> >> >> > > > -- > Paul Rigor > Graduate Student > Institute for Genomics and Bioinformatics > Donald Bren School of Information and Computer Sciences > University of California, Irvine > http://www.paulrigor.net/ > http://www.ics.uci.edu/~prigor > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
