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 -~----------~----~----~----~------~----~------~--~---
