Hi Paul, Actual files for all downloadable resources are saved in biodb, not biodb2. biodb2 has binary files for genomes and NLMSA, and not accessible via http. The files are too big to save in one server...
biodb - only for downloading via http biodb2 - only for accessing via xmlrpc And biodb URLs for public resources. You can download files from below URLs. http://biodb.bioinformatics.ucla.edu/PYGRDATA # for text converted binaries (NLMSA) http://biodb.bioinformatics.ucla.edu/MEGATEST # for megatest files http://biodb.bioinformatics.ucla.edu/GENOMES # for genome assemblies, compressed files Yours, Namshin Kim On Fri, Sep 4, 2009 at 10:20 AM, Paul Rigor (gmail) <paulri...@gmail.com>wrote: > Hi Namshin, > Downloading the genome works for me too. But downloading the multiple > alignment doesn't pull all the necessary resources. > > However, I think you might have missed the latter part of my email in which > I described a possible error with the hard-coded XMLRPC server url which > points to 'biodb' instead of 'biodb2' as you've described in your > instructions on this thread. > > I'm now starting to download the 44way alignment separately. Now even > though I've explicitly set the WORLDBASEPATH to use the 'biodb2' server, > the url still points to 'biodb'. See the log below. So I'm guessing that > the XMLRPC server needs to be updated to reflect the actual locations of the > gzipped picked files. > > Thanks, > Paul > > ===log=== > (2.6.2)06:00 PM 20129 > pri...@mine-17/extra/baldig1/genomics/pygrdata/alignments/human/hg18/multiz44way > $ time python downloadMSA.py > INFO downloader.download_unpickler: Beginning download of > http://biodb.bioinformatics.ucla.edu/PYGRDATA/hg18_multiz44way.txt.gz to > /extra/baldig1/genomics/pygrdata/alignments/human/hg18/multiz44way/hg18_multiz44way.txt.gz... > > INFO downloader.download_monitor: downloaded 7628292096 bytes (10.0%)... > > > On Thu, Sep 3, 2009 at 6:10 PM, Namshin Kim <deepr...@gmail.com> wrote: > >> 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 >>> >>> >>> >> >> >> > > > -- > 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. 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