From dag at sonsorol.org Tue May 11 10:01:20 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue May 11 10:05:21 2004 Subject: [DAS] testing a new Open-Bio website and mail list archive search Message-ID: <40A0DCB0.1050207@sonsorol.org> Hello Everyone, A fantastic volunteer (Kyle Jensen) has been steathily working on a problem for us that has long been a major issue for us -- website searching and indexing. We've tried various solutions and ht://dig implementations in the past and nothing really worked well. Kyle has been setting up a search indexing system based on the code from www.swish-e.org and so far it looks very very promising. We have 2 main indexed search sites: This page is a search index for all of the open-bio hosted websites: http://search.open-bio.org/cgi-bin/obf-search.cgi This page is just for searching mailing list archives: http://search.open-bio.org/cgi-bin/mail-search.cgi Please give the pages a whirl and let me know what you think. Thanks again Kyle! -Chris open-bio.org admin team From lstein at cshl.edu Tue May 11 13:00:08 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Tue May 11 13:04:50 2004 Subject: [DAS] perl module failed test In-Reply-To: <000001c42cc9$f9c28520$f500a8c0@fission> References: <000001c42cc9$f9c28520$f500a8c0@fission> Message-ID: <200405111300.08042.lstein@cshl.edu> Sorry to hear that. Could you tell me what version of Perl you have installed and what operating system this is? Lincoln On Tuesday 27 April 2004 10:38 pm, Michel Dumontier wrote: > Just reporting a failed test on installing the bio-das perl module > (Bio-Das-0.97) from CPAN... > > > Running make test > /usr/bin/perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, > 'blib/lib', 'b lib/arch')" t/*.t > t/01das....ok 22/36Argument "COUNT" isn't numeric in foreach loop > entry at t/01d as.t line 29. > t/01das....FAILED tests 15, 23-36 > Failed 15/36 tests, 58.33% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------- >------------ t/01das.t 36 15 41.67% 15 23-36 > Failed 1/1 test scripts, 0.00% okay. 15/36 subtests failed, 58.33% > okay. make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From td2 at sanger.ac.uk Thu May 13 16:53:35 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Thu May 13 16:57:29 2004 Subject: [DAS] Dazzle 1.01 Message-ID: <99D2EB58-A51F-11D8-B592-000A95C8B056@sanger.ac.uk> Hi, I've just released a new version of Dazzle modular DAS server. It's available from the usual place: http://www.biojava.org/dazzle/ The main change since version 1.00 is the addition of a new plugin which allows Dazzle annotation servers to be set up backed by SQL databases in the LDAS format. Instructions for using LdasDataSource can be found at the bottom of the deployment guide. The plugin API is unchanged since 1.00 Thomas. From seanok at gsf.de Mon May 17 11:53:33 2004 From: seanok at gsf.de (Sean O'Keeffe) Date: Mon May 17 15:41:34 2004 Subject: [DAS] trouble attaching das source Message-ID: <40A8DFFD.9060405@gsf.de> Hi there, I'm a bioinformatics researcher at the GSF national research institute in munich, germany. I have set-up a das server (dazzle 0.97a) according to instructions on the ensembl site. It seems fine and shows up all the data-sources when I point to the das server. My problem arises when i try to attach the server to the ensembl web site - click on 'manage sources' on the das sources tab in contig view. Nothing happens when i type in our server 'andromeda.gsf.de:7070' and click on "show sources" - after about 5-10 seconds it just refreshes and is blank. I had it running fine on a previous ensembl version but this is now version 20 and we've added extra data here also. My dazzle config xml file (part of it) is below: Any help would be great. Thanks, Sean. From td2 at sanger.ac.uk Mon May 17 16:33:15 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Mon May 17 16:36:51 2004 Subject: [DAS] trouble attaching das source In-Reply-To: <40A8DFFD.9060405@gsf.de> References: <40A8DFFD.9060405@gsf.de> Message-ID: <6C78CFE6-A841-11D8-AD85-000A95C8B056@sanger.ac.uk> Hi Sean, I'm afraid the version 20 databases include some major changed to the schema. Updating the old biojava-ensembl and ensembl-das code wasn't going to be practical, since a lot of the internal assumptions about how assemblies work, etc., have been broken. I've written some new code which should do the job -- unfortunately I haven't had a chance to put together a release yet. But you can get the latest code using Subversion (http://subversion.tigris.org/) from: http://www.derkholm.net/svn/repos/biojava-ensembl/trunk/ Or send me an e-mail directly if you'd prefer me to send you a snapshot. This includes both some new biojava-ensembl bridge code which can handle both schema-20+ and old-format database, and a new set of ensembl-das plugins which are compatible with dazzle 1.0x: http://www.biojava.org/dazzle/ A typical configuration for the new system looks something like: Sorry I've been so slow getting this properly released -- give me a shout if you need any help with it, Thomas. On 17 May 2004, at 16:53, Sean O'Keeffe wrote: > Hi there, > I'm a bioinformatics researcher at the GSF national research institute > in munich, germany. > I have set-up a das server (dazzle 0.97a) according to instructions on > the ensembl site. > It seems fine and shows up all the data-sources when I point to the > das server. > My problem arises when i try to attach the server to the ensembl web > site - click on 'manage sources' on the das sources tab in contig > view. Nothing happens when i type in our server > 'andromeda.gsf.de:7070' and click on "show sources" - after about 5-10 > seconds it just refreshes and is blank. > I had it running fine on a previous ensembl version but this is now > version 20 and we've added extra data here also. > My dazzle config xml file (part of it) is below: > Any help would be great. > Thanks, Sean. > > > > > > > value="jdbc:mysql://andromeda.gsf.de/mus_musculus_core_20_32b" /> > > > > > > > > > > > > > > > > > > jclass="ensembl.EnsemblGenericSeqFeatureSource"> > > > > > value="http://andromeda.gsf.de:7070/das/mouse2032b/" /> > value="jdbc:mysql://andromeda.gsf.de/ensembl_generic/" /> > > > > > > > > _______________________________________________ > DAS mailing list > DAS@biodas.org > http://biodas.org/mailman/listinfo/das From hxu at chg.duhs.duke.edu Mon May 17 16:50:25 2004 From: hxu at chg.duhs.duke.edu (Hong Xu) Date: Tue May 18 10:23:05 2004 Subject: [DAS] trouble attaching das source References: <40A8DFFD.9060405@gsf.de> <6C78CFE6-A841-11D8-AD85-000A95C8B056@sanger.ac.uk> Message-ID: <006901c43c50$94d7aff0$954c1098@DNA319> So what's the DAS server Ensembl is using on its site? Is it a modified version of dazzle, LDAS, or ProServer? I need to find out this before I update our local Ensembl to the latest release. thanks, Hong Xu +1 919 684 3962 hong.xu@duke.edu wwwchg.duhs.duke.edu ----- Original Message ----- From: "Thomas Down" To: "Sean O'Keeffe" Cc: Sent: Monday, May 17, 2004 4:33 PM Subject: Re: [DAS] trouble attaching das source > Hi Sean, > > I'm afraid the version 20 databases include some major changed to the > schema. Updating the old biojava-ensembl and ensembl-das code wasn't > going to be practical, since a lot of the internal assumptions about > how assemblies work, etc., have been broken. > > I've written some new code which should do the job -- unfortunately I > haven't had a chance to put together a release yet. But you can get > the latest code using Subversion (http://subversion.tigris.org/) from: > > http://www.derkholm.net/svn/repos/biojava-ensembl/trunk/ > > Or send me an e-mail directly if you'd prefer me to send you a snapshot. > > This includes both some new biojava-ensembl bridge code which can > handle both schema-20+ and old-format database, and a new set of > ensembl-das plugins which are compatible with dazzle 1.0x: > > http://www.biojava.org/dazzle/ > > A typical configuration for the new system looks something like: > > > jclass="org.ensembl.das.DatabaseHolder"> > value="jdbc:mysql://noranti/homo_sapiens_core_20_34b" /> > > > > > jclass="org.ensembl.das.EnsemblCoreReference"> > > > > > > > > value="http://www.ensembl.org/Homo_sapiens/" /> > > > > > Sorry I've been so slow getting this properly released -- give me a > shout if you need any help with it, > > Thomas. > > > > On 17 May 2004, at 16:53, Sean O'Keeffe wrote: > > > Hi there, > > I'm a bioinformatics researcher at the GSF national research institute > > in munich, germany. > > I have set-up a das server (dazzle 0.97a) according to instructions on > > the ensembl site. > > It seems fine and shows up all the data-sources when I point to the > > das server. > > My problem arises when i try to attach the server to the ensembl web > > site - click on 'manage sources' on the das sources tab in contig > > view. Nothing happens when i type in our server > > 'andromeda.gsf.de:7070' and click on "show sources" - after about 5-10 > > seconds it just refreshes and is blank. > > I had it running fine on a previous ensembl version but this is now > > version 20 and we've added extra data here also. > > My dazzle config xml file (part of it) is below: > > Any help would be great. > > Thanks, Sean. > > > > > > > > > > > > > > > value="jdbc:mysql://andromeda.gsf.de/mus_musculus_core_20_32b" /> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > jclass="ensembl.EnsemblGenericSeqFeatureSource"> > > > > > > > > > > > value="http://andromeda.gsf.de:7070/das/mouse2032b/" /> > > > value="jdbc:mysql://andromeda.gsf.de/ensembl_generic/" /> > > > > > > > > > > > > > > > > _______________________________________________ > > DAS mailing list > > DAS@biodas.org > > http://biodas.org/mailman/listinfo/das > > _______________________________________________ > DAS mailing list > DAS@biodas.org > http://biodas.org/mailman/listinfo/das > From td2 at sanger.ac.uk Tue May 18 12:48:25 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue May 18 12:51:58 2004 Subject: [DAS] trouble attaching das source In-Reply-To: <006901c43c50$94d7aff0$954c1098@DNA319> References: <40A8DFFD.9060405@gsf.de> <6C78CFE6-A841-11D8-AD85-000A95C8B056@sanger.ac.uk> <006901c43c50$94d7aff0$954c1098@DNA319> Message-ID: <2E4D4678-A8EB-11D8-9661-000A95C8B056@sanger.ac.uk> I'm not the best person to confirm this, but as far as I know all three servers are being used, for different types of data. (You might be interested to look at release 1.01 of Dazzle, which includes a plugin to serve data from the same Bio::DB::GFF databases which LDAS uses) Thomas On 17 May 2004, at 21:50, Hong Xu wrote: > So what's the DAS server Ensembl is using on its site? Is it a modified > version of dazzle, LDAS, or ProServer? I need to find out this before I > update our local Ensembl to the latest release. > > thanks, > Hong Xu +1 919 684 3962 > hong.xu@duke.edu wwwchg.duhs.duke.edu > > > ----- Original Message ----- > From: "Thomas Down" > To: "Sean O'Keeffe" > Cc: > Sent: Monday, May 17, 2004 4:33 PM > Subject: Re: [DAS] trouble attaching das source > > >> Hi Sean, >> >> I'm afraid the version 20 databases include some major changed to the >> schema. Updating the old biojava-ensembl and ensembl-das code wasn't >> going to be practical, since a lot of the internal assumptions about >> how assemblies work, etc., have been broken. >> >> I've written some new code which should do the job -- unfortunately I >> haven't had a chance to put together a release yet. But you can get >> the latest code using Subversion (http://subversion.tigris.org/) from: >> >> http://www.derkholm.net/svn/repos/biojava-ensembl/trunk/ >> >> Or send me an e-mail directly if you'd prefer me to send you a >> snapshot. >> >> This includes both some new biojava-ensembl bridge code which can >> handle both schema-20+ and old-format database, and a new set of >> ensembl-das plugins which are compatible with dazzle 1.0x: >> >> http://www.biojava.org/dazzle/ >> >> A typical configuration for the new system looks something like: >> >> >> > jclass="org.ensembl.das.DatabaseHolder"> >> > value="jdbc:mysql://noranti/homo_sapiens_core_20_34b" /> >> >> >> >> >> > jclass="org.ensembl.das.EnsemblCoreReference"> >> >> >> >> >> >> >> >> > value="http://www.ensembl.org/Homo_sapiens/" /> >> >> >> >> >> Sorry I've been so slow getting this properly released -- give me a >> shout if you need any help with it, >> >> Thomas. >> >> >> >> On 17 May 2004, at 16:53, Sean O'Keeffe wrote: >> >>> Hi there, >>> I'm a bioinformatics researcher at the GSF national research >>> institute >>> in munich, germany. >>> I have set-up a das server (dazzle 0.97a) according to instructions >>> on >>> the ensembl site. >>> It seems fine and shows up all the data-sources when I point to the >>> das server. >>> My problem arises when i try to attach the server to the ensembl web >>> site - click on 'manage sources' on the das sources tab in contig >>> view. Nothing happens when i type in our server >>> 'andromeda.gsf.de:7070' and click on "show sources" - after about >>> 5-10 >>> seconds it just refreshes and is blank. >>> I had it running fine on a previous ensembl version but this is now >>> version 20 and we've added extra data here also. >>> My dazzle config xml file (part of it) is below: >>> Any help would be great. >>> Thanks, Sean. >>> >>> >>> >>> >>> >>> >>> >> value="jdbc:mysql://andromeda.gsf.de/mus_musculus_core_20_32b" /> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> /> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> jclass="ensembl.EnsemblGenericSeqFeatureSource"> >>> >>> >>> >>> >>> >> value="http://andromeda.gsf.de:7070/das/mouse2032b/" /> >>> >> value="jdbc:mysql://andromeda.gsf.de/ensembl_generic/" /> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> DAS mailing list >>> DAS@biodas.org >>> http://biodas.org/mailman/listinfo/das >> >> _______________________________________________ >> DAS mailing list >> DAS@biodas.org >> http://biodas.org/mailman/listinfo/das >> > > _______________________________________________ > DAS mailing list > DAS@biodas.org > http://biodas.org/mailman/listinfo/das >