From m.pheasant at imb.uq.edu.au Mon Aug 6 04:28:30 2007 From: m.pheasant at imb.uq.edu.au (Michael Pheasant) Date: Mon, 06 Aug 2007 21:28:30 +1000 Subject: [Genome-mirror] rsync errors Message-ID: Hi, I'm getting some rsync errors from rsync://hgdownload.cse.ucsc.edu/genome/ Looks like file permissions on your end? cheers Mike rsync: readlink "/goldenPath/droVir3/bigZips/README.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.agp.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.fa.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.fa.masked.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.fa.out.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.trf.bed.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droVir3/bigZips/md5sum.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/README.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.fa.masked.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.agp.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.fa.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.fa.out.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.trf.bed.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droMoj3/bigZips/md5sum.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/README.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.agp.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.fa.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.fa.masked.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.fa.out.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.trf.bed.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droWil1/bigZips/md5sum.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/README.txt" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.agp.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.fa.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.fa.masked.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.fa.out.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.trf.bed.gz" (in genome) failed: Permission denied (13) rsync: readlink "/goldenPath/droGri2/bigZips/md5sum.txt" (in genome) failed: Permission denied (13) __________________________________ Michael Pheasant, PhD Bioinformatics Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4067 Australia P: +61-7-3346-2080 M: +61-405-679-541 http://www.imb.uq.edu.au From jgarcia at soe.ucsc.edu Mon Aug 6 10:29:39 2007 From: jgarcia at soe.ucsc.edu (Jorge Garcia) Date: Mon, 06 Aug 2007 10:29:39 -0700 Subject: [Genome-mirror] rsync errors In-Reply-To: References: Message-ID: <46B75A83.2020204@soe.ucsc.edu> This should be fixed now. Jorge Michael Pheasant wrote: > Hi, > > I'm getting some rsync errors from rsync://hgdownload.cse.ucsc.edu/genome/ > Looks like file permissions on your end? > > cheers > > Mike > > rsync: readlink "/goldenPath/droVir3/bigZips/README.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.agp.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.fa.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.fa.masked.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.fa.out.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droVir3/bigZips/droVir3.trf.bed.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droVir3/bigZips/md5sum.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/README.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.fa.masked.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.agp.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.fa.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.fa.out.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/droMoj3.trf.bed.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droMoj3/bigZips/md5sum.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/README.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.agp.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.fa.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.fa.masked.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.fa.out.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/droWil1.trf.bed.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droWil1/bigZips/md5sum.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/README.txt" (in genome) failed: > Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.agp.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.fa.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.fa.masked.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.fa.out.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/droGri2.trf.bed.gz" (in genome) > failed: Permission denied (13) > rsync: readlink "/goldenPath/droGri2/bigZips/md5sum.txt" (in genome) failed: > Permission denied (13) > > > > __________________________________ > Michael Pheasant, PhD > Bioinformatics Research > Institute for Molecular Bioscience > The University of Queensland > Brisbane QLD 4067 Australia > P: +61-7-3346-2080 > M: +61-405-679-541 > http://www.imb.uq.edu.au > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From aamp at ucsc.edu Fri Aug 10 15:05:41 2007 From: aamp at ucsc.edu (Andy Pohl) Date: Fri, 10 Aug 2007 15:05:41 -0700 Subject: [Genome-mirror] v165 Genome Browser Available Message-ID: <9fa943760708101505k1028a5bck52c9169592b959a6@mail.gmail.com> Hello, The v165 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v165.zip cartDump cartReset das hgc hgBlat hgConvert hgCustom hgEncodeDataVersions hgGateway hgGene hgGenome hgLiftOver hgNear hgPcr hgSession hgTables hgText hgTracks hgTrackUi hgVisiGene mkEncodeFrameset pbGateway pbGlobal pbTracks phyloGif /usr/local/apache/cgi-bin/all.joiner /usr/local/apache/cgi-bin/hgNearData/* /usr/local/apache/cgi-bin/hgGeneData/* /usr/local/apache/cgi-bin/hgcData/* /usr/local/apache/cgi-bin/hgCgiData/* /usr/local/apache/cgi-bin/loader/* /usr/local/apache/cgi-bin/visiGeneData/* Contents of v165 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v165-preview and v165-final to see all the code and data changes in this release. Have a nice weekend! Andy Pohl UCSC CBSE From vcpatel at genetics.emory.edu Wed Aug 15 10:00:00 2007 From: vcpatel at genetics.emory.edu (Viren Patel) Date: Wed, 15 Aug 2007 13:00:00 -0400 Subject: [Genome-mirror] proteome browser not working Message-ID: <46C33110.1080106@genetics.emory.edu> Hello. I have setup a mirror of the UCSC genome browser in my department using instructions at http://genome.ucsc.edu/admin/mirror.html. When testing the proteome browser I get the following error: Can't start query: select val from sp070202.protein where acc='O15391'; In looking at the proteins070202 database I don't see a protein table. It's also not there in the proteins060115 database. It seems I may have missed some steps in the setup of the protein databases but I can't see anything obvious from the instructions. Any pointers? Thanks. Viren Patel Department of Human Genetics Emory University School of Medicine From fanhsu at soe.ucsc.edu Wed Aug 15 14:56:06 2007 From: fanhsu at soe.ucsc.edu (Fan Hsu) Date: Wed, 15 Aug 2007 14:56:06 -0700 Subject: [Genome-mirror] proteome browser not working In-Reply-To: <46C33110.1080106@genetics.emory.edu> Message-ID: Hi Viren, There should be two symbolic links: proteome -> proteins070202 uniProt -> sp070202 under your /var/lib/mysql. Please check if your system has those. Fan. -----Original Message----- From: genome-mirror-bounces at soe.ucsc.edu [mailto:genome-mirror-bounces at soe.ucsc.edu]On Behalf Of Viren Patel Sent: Wednesday, August 15, 2007 10:00 AM To: genome-mirror at soe.ucsc.edu Subject: [Genome-mirror] proteome browser not working Hello. I have setup a mirror of the UCSC genome browser in my department using instructions at http://genome.ucsc.edu/admin/mirror.html. When testing the proteome browser I get the following error: Can't start query: select val from sp070202.protein where acc='O15391'; In looking at the proteins070202 database I don't see a protein table. It's also not there in the proteins060115 database. It seems I may have missed some steps in the setup of the protein databases but I can't see anything obvious from the instructions. Any pointers? Thanks. Viren Patel Department of Human Genetics Emory University School of Medicine _______________________________________________ Genome-mirror mailing list Genome-mirror at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From vcpatel at genetics.emory.edu Thu Aug 16 05:18:07 2007 From: vcpatel at genetics.emory.edu (Viren Patel) Date: Thu, 16 Aug 2007 08:18:07 -0400 Subject: [Genome-mirror] proteome browser not working In-Reply-To: References: Message-ID: <46C4407F.9070001@genetics.emory.edu> Thanks. I think you mean sp070202 -> uniProt. This is missing in the mirror instructions. Also had to grant privileges on those to database user. Viren Fan Hsu wrote: > Hi Viren, > > There should be two symbolic links: > > proteome -> proteins070202 > uniProt -> sp070202 > > under your /var/lib/mysql. Please check if your system has those. > > Fan. > -----Original Message----- > From: genome-mirror-bounces at soe.ucsc.edu > [mailto:genome-mirror-bounces at soe.ucsc.edu]On Behalf Of Viren Patel > Sent: Wednesday, August 15, 2007 10:00 AM > To: genome-mirror at soe.ucsc.edu > Subject: [Genome-mirror] proteome browser not working > > > Hello. I have setup a mirror of the UCSC genome browser in my department > using instructions at http://genome.ucsc.edu/admin/mirror.html. When > testing the proteome browser I get the following error: > > Can't start query: select val from sp070202.protein where acc='O15391'; > > In looking at the proteins070202 database I don't see a protein table. > It's also not there in the proteins060115 database. It seems I may have > missed some steps in the setup of the protein databases but I can't see > anything obvious from the instructions. Any pointers? Thanks. > > Viren Patel > Department of Human Genetics > Emory University School of Medicine > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From ann at soe.ucsc.edu Thu Aug 16 11:08:11 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Thu, 16 Aug 2007 11:08:11 -0700 Subject: [Genome-mirror] proteome browser not working In-Reply-To: <46C4407F.9070001@genetics.emory.edu> References: <46C4407F.9070001@genetics.emory.edu> Message-ID: <46C4928B.7070505@soe.ucsc.edu> Hello Viren, Thanks for the details. We are always looking for input on the mirror instructions. We have added the instructions about the uniProt symlink. Thanks, Ann Zweig. Viren Patel wrote: > Thanks. I think you mean sp070202 -> uniProt. This is missing in the > mirror instructions. Also had to grant privileges on those to database user. > > Viren > > Fan Hsu wrote: >> Hi Viren, >> >> There should be two symbolic links: >> >> proteome -> proteins070202 >> uniProt -> sp070202 >> >> under your /var/lib/mysql. Please check if your system has those. >> >> Fan. >> -----Original Message----- >> From: genome-mirror-bounces at soe.ucsc.edu >> [mailto:genome-mirror-bounces at soe.ucsc.edu]On Behalf Of Viren Patel >> Sent: Wednesday, August 15, 2007 10:00 AM >> To: genome-mirror at soe.ucsc.edu >> Subject: [Genome-mirror] proteome browser not working >> >> >> Hello. I have setup a mirror of the UCSC genome browser in my department >> using instructions at http://genome.ucsc.edu/admin/mirror.html. When >> testing the proteome browser I get the following error: >> >> Can't start query: select val from sp070202.protein where acc='O15391'; >> >> In looking at the proteins070202 database I don't see a protein table. >> It's also not there in the proteins060115 database. It seems I may have >> missed some steps in the setup of the protein databases but I can't see >> anything obvious from the instructions. Any pointers? Thanks. >> >> Viren Patel >> Department of Human Genetics >> Emory University School of Medicine >> >> >> _______________________________________________ >> Genome-mirror mailing list >> Genome-mirror at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >> > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From kayla at soe.ucsc.edu Thu Aug 16 17:08:48 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Thu, 16 Aug 2007 17:08:48 -0700 Subject: [Genome-mirror] Release of new assembly: Cow (BosTau3) Message-ID: <46C4E710.6030605@cse.ucsc.edu> Hello mirror sites, We are intending to release the new cow assembly, bosTau3, next week. Mirror sites should be prepared to host the following data: ~ 14.1G bosTau3 tables ~ 4.2G /gbdb/bosTau3/* files Additionally, there are cow net and chain tables (called netBosTau3 and *chainBosTau3*) from other organisms that will be released to their respective annotation databases. The sizes of these tables are as follows: hg18 4.5 G mm8 2.5 G rn4 2.5 G ================= total 9.5 G tables in other assemblies (these are replacing the older chain/net bosTau2 tables) Grand total: ~27.8G of new data. Please let us know if you have any questions or concerns. Kayla Smith UCSC Genome Bioinformatics Group From archanat at soe.ucsc.edu Fri Aug 17 14:19:29 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Fri, 17 Aug 2007 14:19:29 -0700 Subject: [Genome-mirror] Release of new assembly: Mouse ( mm9 ) Message-ID: <46C610E1.2020809@soe.ucsc.edu> Hello mirror sites, This message is to announce that we are preparing to release the new Mouse assembly, mm9, next week. Mirror sites should be prepared to host: ~7 Gb ( mm9 tables ) ~1.7 Gb ( files in /gbdb/mm9/* ) Please let us know if you have any questions or concerns. Thanks, Archana UCSC Genome Bioinformatics Group From thomas at tll.org.sg Fri Aug 17 23:37:30 2007 From: thomas at tll.org.sg (Thomas Sandmann) Date: Sat, 18 Aug 2007 14:37:30 +0800 Subject: [Genome-mirror] fixing link in partial mirror of the UCSC genome browser Message-ID: <1187419050.6871.9.camel@Linux-cohen1> Dear UCSC browser team, I have successfully mirrored the UCSC browser with just the dm2 and dm3 datasets locally. Things work fine, except for the html page that is normally opened when clicking on a specific gene in the "flybase genes" track. Instead of the usual page displaying information about the locus, e.g. as in http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=CG11611-RA&hgg_chrom=chr3L&hgg_start=11767233&hgg_end=11767512&hgg_type=flyBaseGene&db=dm3&hgsid=96007445 the "genome.ra" file is reported to be missing. I have tracked it down in the hgGeneData folder and copied the whole folder into the cgi-bin directory. Still the link doesn't work and now I get the following error instead: "Couldn't connect to database uniProt on localhost as readonly. Access denied for user 'readonly'@'localhost' to database 'uniProt'" No surprise, as I did not mirror the uniprot database... Obviously, my minimal installation misses a number of mysql tables to generate the html page. Is there a way for me to get the link to work without mirroring a lot of data unrelated to my chosen Drosophila datasets ? Maybe you could point out the absolutely necessary tables to me ? Thanks a lot ! Thomas From fanhsu at soe.ucsc.edu Sat Aug 18 09:16:29 2007 From: fanhsu at soe.ucsc.edu (Fan Hsu) Date: Sat, 18 Aug 2007 09:16:29 -0700 Subject: [Genome-mirror] fixing link in partial mirror of the UCSC genomebrowser In-Reply-To: <1187419050.6871.9.camel@Linux-cohen1> Message-ID: Hi Thomas, The cheapest solution probably is to just install the uniProt and proteome DBs on your system. They should not occupy more that 15 GB. Otherwise, you are talking about hours/days of someone's time to modify the src (which would be messy and you should stay away from this) or selectively copying of tables with try and error, which also cost time. Fan. -----Original Message----- From: genome-mirror-bounces at soe.ucsc.edu [mailto:genome-mirror-bounces at soe.ucsc.edu]On Behalf Of Thomas Sandmann Sent: Friday, August 17, 2007 11:38 PM To: genome-mirror at soe.ucsc.edu Subject: [Genome-mirror] fixing link in partial mirror of the UCSC genomebrowser Dear UCSC browser team, I have successfully mirrored the UCSC browser with just the dm2 and dm3 datasets locally. Things work fine, except for the html page that is normally opened when clicking on a specific gene in the "flybase genes" track. Instead of the usual page displaying information about the locus, e.g. as in http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=CG11611-RA&hgg_chrom=chr3L&hg g_start=11767233&hgg_end=11767512&hgg_type=flyBaseGene&db=dm3&hgsid=96007445 the "genome.ra" file is reported to be missing. I have tracked it down in the hgGeneData folder and copied the whole folder into the cgi-bin directory. Still the link doesn't work and now I get the following error instead: "Couldn't connect to database uniProt on localhost as readonly. Access denied for user 'readonly'@'localhost' to database 'uniProt'" No surprise, as I did not mirror the uniprot database... Obviously, my minimal installation misses a number of mysql tables to generate the html page. Is there a way for me to get the link to work without mirroring a lot of data unrelated to my chosen Drosophila datasets ? Maybe you could point out the absolutely necessary tables to me ? Thanks a lot ! Thomas _______________________________________________ Genome-mirror mailing list Genome-mirror at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From angie at soe.ucsc.edu Sat Aug 18 09:49:07 2007 From: angie at soe.ucsc.edu (Angie Hinrichs) Date: Sat, 18 Aug 2007 09:49:07 -0700 (PDT) Subject: [Genome-mirror] fixing link in partial mirror of the UCSC genomebrowser In-Reply-To: References: Message-ID: Hi Thomas, There is another alternative that is easier, but then you'll miss out on the nice displays that hgGene has -- you can choose to just see a minimal details page about the gene. Here's how to do that if you wish. In these two files: kent/src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra kent/src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra look for the track description for flyBaseGene, and remove the directUrl line: track flyBaseGene ... directUrl ../cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s Then, in trackDb/, run this command: make alpha DBS='dm2 dm3' That reads the trackDb.ra files and reloads the trackDb tables in dm2 and dm3, so that they no longer specify hgGene for FlyBase Genes. In order for the make alpha to successfully reload the trackDb tables, you will need a ~/.hg.conf file that is readable/writable only by you, and that looks like cgi-bin/hg.conf but contains a mysql username and password that are allowed to create, insert and drop tables. [Having a ~/.hg.conf also enables you to run cgi-bin programs on the command line, very useful for debugging error 500s.] Angie On Sat, 18 Aug 2007, Fan Hsu wrote: > Hi Thomas, > > The cheapest solution probably is to just install the uniProt and proteome > DBs > on your system. They should not occupy more that 15 GB. > > Otherwise, you are talking about hours/days of someone's time to > modify the src (which would be messy and you should stay away from this) > or selectively copying of tables with try and error, which also cost time. > > Fan. > -----Original Message----- > From: genome-mirror-bounces at soe.ucsc.edu > [mailto:genome-mirror-bounces at soe.ucsc.edu]On Behalf Of Thomas Sandmann > Sent: Friday, August 17, 2007 11:38 PM > To: genome-mirror at soe.ucsc.edu > Subject: [Genome-mirror] fixing link in partial mirror of the UCSC > genomebrowser > > > Dear UCSC browser team, > > I have successfully mirrored the UCSC browser with just the dm2 and dm3 > datasets locally. Things work fine, except for the html page that is > normally opened when clicking on a specific gene in the "flybase genes" > track. Instead of the usual page displaying information about the locus, > e.g. as in > http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=CG11611-RA&hgg_chrom=chr3L&hg > g_start=11767233&hgg_end=11767512&hgg_type=flyBaseGene&db=dm3&hgsid=96007445 > > the "genome.ra" file is reported to be missing. I have tracked it down > in the hgGeneData folder and copied the whole folder into the cgi-bin > directory. Still the link doesn't work and now I get the following error > instead: > "Couldn't connect to database uniProt on localhost as readonly. Access > denied for user 'readonly'@'localhost' to database 'uniProt'" > > No surprise, as I did not mirror the uniprot database... > Obviously, my minimal installation misses a number of mysql tables to > generate the html page. Is there a way for me to get the link to work > without mirroring a lot of data unrelated to my chosen Drosophila > datasets ? Maybe you could point out the absolutely necessary tables to > me ? > > Thanks a lot ! > Thomas > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > -- angie at soe.ucsc.edu Software Developer, UCSC CBSE / Genome Bioinformatics Group From jlchang at broad.mit.edu Mon Aug 20 12:23:46 2007 From: jlchang at broad.mit.edu (Jean Chang) Date: Mon, 20 Aug 2007 15:23:46 -0400 Subject: [Genome-mirror] gfServer for isPCR and minRep question Message-ID: <19D4E4BA-5365-4180-B8AC-DF7E3076FABA@broad.mit.edu> Hi all, We have sets of primers that we've designed on the human genome that we're sanity-checking using our local isPCR. We've noticed that some primer sets are coming back with no matches. The one thing all these failed primer sets have in common is that at least one primer is softmasked - but not all softmasked primers fail. Does gfServer had a default repeat masking behaviour? The usage message would suggest so: -repMatch=N Number of occurrences of a tile (nmer) that trigger repeat masking the tile. Default is 1024. If my interpretation is correct, what would be the syntax for turning masking off completely? I notice that blat does not use repMatch unless -makeOoc is invoked so I'm hoping that no masking is acceptable. If not masking will cause problems, what is the highest recommended setting for repMatch? Thanks, jean From kayla at soe.ucsc.edu Tue Aug 21 15:17:09 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 21 Aug 2007 15:17:09 -0700 Subject: [Genome-mirror] gfServer for isPCR and minRep question In-Reply-To: <19D4E4BA-5365-4180-B8AC-DF7E3076FABA@broad.mit.edu> References: <19D4E4BA-5365-4180-B8AC-DF7E3076FABA@broad.mit.edu> Message-ID: <46CB6465.809@cse.ucsc.edu> Hello Jean, One of our developers is suggesting that you try to use a very big number for repMatch. Something on the order of 1,000,000. Let me know if you still have questions after trying this. Kayla Smith UCSC Genome Bioinformatics Group Jean Chang wrote: > Hi all, > > We have sets of primers that we've designed on the human genome that > we're sanity-checking using our local isPCR. We've noticed that some > primer sets are coming back with no matches. The one thing all these > failed primer sets have in common is that at least one primer is > softmasked - but not all softmasked primers fail. > > Does gfServer had a default repeat masking behaviour? The usage > message would suggest so: > > -repMatch=N Number of occurrences of a tile (nmer) that trigger > repeat masking the tile. > Default is 1024. > > If my interpretation is correct, what would be the syntax for turning > masking off completely? I notice that blat does not use repMatch > unless -makeOoc is invoked so I'm hoping that no masking is > acceptable. If not masking will cause problems, what is the highest > recommended setting for repMatch? > > Thanks, > > jean > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From vcpatel at genetics.emory.edu Wed Aug 22 07:42:41 2007 From: vcpatel at genetics.emory.edu (Viren Patel) Date: Wed, 22 Aug 2007 10:42:41 -0400 Subject: [Genome-mirror] mysql database file permissions Message-ID: <46CC4B61.6090005@genetics.emory.edu> I have adapted the script from https://www.soe.ucsc.edu/pipermail/genome-mirror/2007-March/000379.html to sync our mirror. However I am getting "permission denied" errors when updating mysql database tables, e.g. rsync: send_files failed to open "/danRer3/affyZebrafish.MYD" (in mysql): Permission denied (13) The MySQL directory, subdirs, and files are owned mysql:mysql with permissions set to 700 on directories and 660 on files. I am running the sync script as root, which is why I don't understand the errors. Any ideas? Thanks. Viren Department of Human Genetics Emory University School of Medicine From michaelw at onlinehome.de Sun Aug 26 02:12:47 2007 From: michaelw at onlinehome.de (Wagner, Michael) Date: Sun, 26 Aug 2007 11:12:47 +0200 Subject: [Genome-mirror] GNF Expression Atlas Message-ID: <46D1440F.7000707@onlinehome.de> Dear Ladies and Gentlemen, I've just a simple question to the color shemes of the GNF Expression Atlas and I didn't find the answer at tha FAQ's. There are several greysteps for absolut expression from dark grey to lightgrey. I just want to know which of them stands for no expression and which one for high expression. As I said before, I wasn't lucky to find the explanation on your page. I thank you very much for your help. Kind regards, Michael Wagner From kayla at soe.ucsc.edu Mon Aug 27 11:21:08 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Mon, 27 Aug 2007 11:21:08 -0700 Subject: [Genome-mirror] GNF Expression Atlas In-Reply-To: <46D1440F.7000707@onlinehome.de> References: <46D1440F.7000707@onlinehome.de> Message-ID: <46D31614.30904@cse.ucsc.edu> Hello Michael, Here's a link to some information on the GNF Atlas 2 data: http://genome.ucsc.edu/cgi-bin/hgNear?near.do.colInfo=gnfHumanAtlas2 I hope this is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Wagner, Michael wrote: > Dear Ladies and Gentlemen, > > I've just a simple question to the color shemes of the GNF Expression > Atlas and I didn't find the answer at tha FAQ's. There are several > greysteps for absolut expression from dark grey to lightgrey. I just > want to know which of them stands for no expression and which one for > high expression. As I said before, I wasn't lucky to find the > explanation on your page. I thank you very much for your help. > > Kind regards, > > Michael Wagner > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From ann at soe.ucsc.edu Tue Aug 28 09:25:59 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Tue, 28 Aug 2007 09:25:59 -0700 Subject: [Genome-mirror] safe to drop several tables Message-ID: <46D44C97.1060306@soe.ucsc.edu> Hello Mirror Sites, We have replaced mm8 nets and chains with mm9 nets and chains on the hg18 and rn4 assemblies. Consequently, after you rsync, it is safe to drop the following tables: from the hg18 database: (this is a total of 99 tables) netMm8 chr*_chainMm8Link chr*_chainMm8 from the rn4 database: (this is a total of 91 tables) netMm8 chr*_chainMm8Link chr*_chainMm8 Regards, Ann Zweig. From kayla at soe.ucsc.edu Wed Aug 29 12:20:24 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Wed, 29 Aug 2007 12:20:24 -0700 Subject: [Genome-mirror] some cow tables can be dropped Message-ID: <46D5C6F8.9050806@cse.ucsc.edu> Good afternoon Mirror Sites: There are new chain and net tables to bosTau3, replacing the old ones to bosTau2. It is safe to delete the following tables from the following databases: hg18: netBosTau2 *chainBosTau2 *chainBosTau2Link mm8: netBosTau2 *chainBosTau2 *chainBosTau2Link rn4: netBosTau2 *chainBosTau2 *chainBosTau2Link Thanks, Kayla Smith UCSC Genome Bioinformatics Group From tsfurey at duke.edu Thu Aug 30 06:35:34 2007 From: tsfurey at duke.edu (Terry Furey) Date: Thu, 30 Aug 2007 09:35:34 -0400 (EDT) Subject: [Genome-mirror] some cow tables can be dropped In-Reply-To: <46D5C6F8.9050806@cse.ucsc.edu> References: <46D5C6F8.9050806@cse.ucsc.edu> Message-ID: Hi Kayla - I appreciate the updates like this very much. Previously, I believe we were told that we could remove the mm8 chain and net tables from hg18 and rn4. I did this yesterday, and they all came back last night. Can you confirm that these have been removed from the rsync server? Thanks, Terry On Wed, 29 Aug 2007, Kayla Smith wrote: > > Good afternoon Mirror Sites: > > There are new chain and net tables to bosTau3, replacing the old ones to > bosTau2. It is safe to delete the following tables from the following > databases: > > hg18: > netBosTau2 > *chainBosTau2 > *chainBosTau2Link > > mm8: > netBosTau2 > *chainBosTau2 > *chainBosTau2Link > > rn4: > netBosTau2 > *chainBosTau2 > *chainBosTau2Link > > > Thanks, > > Kayla Smith > UCSC Genome Bioinformatics Group > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From ann at soe.ucsc.edu Thu Aug 30 09:58:05 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Thu, 30 Aug 2007 09:58:05 -0700 Subject: [Genome-mirror] some cow tables can be dropped In-Reply-To: References: <46D5C6F8.9050806@cse.ucsc.edu> Message-ID: <46D6F71D.8050303@soe.ucsc.edu> Hello Terry, I'm the one who let you know you could drop those tables. And that was correct. However, I see what you're saying -- they are still on hgdownload. I will look into this today. Regards, Ann Zweig. Terry Furey wrote: > Hi Kayla - > > I appreciate the updates like this very much. Previously, I believe we > were told that we could remove the mm8 chain and net tables from hg18 and > rn4. I did this yesterday, and they all came back last night. Can you > confirm that these have been removed from the rsync server? > > Thanks, > > Terry > > On Wed, 29 Aug 2007, Kayla Smith wrote: > >> Good afternoon Mirror Sites: >> >> There are new chain and net tables to bosTau3, replacing the old ones to >> bosTau2. It is safe to delete the following tables from the following >> databases: >> >> hg18: >> netBosTau2 >> *chainBosTau2 >> *chainBosTau2Link >> >> mm8: >> netBosTau2 >> *chainBosTau2 >> *chainBosTau2Link >> >> rn4: >> netBosTau2 >> *chainBosTau2 >> *chainBosTau2Link >> >> >> Thanks, >> >> Kayla Smith >> UCSC Genome Bioinformatics Group >> _______________________________________________ >> Genome-mirror mailing list >> Genome-mirror at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >> > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From ann at soe.ucsc.edu Thu Aug 30 13:23:15 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Thu, 30 Aug 2007 13:23:15 -0700 Subject: [Genome-mirror] some cow tables can be dropped In-Reply-To: <46D6F71D.8050303@soe.ucsc.edu> References: <46D5C6F8.9050806@cse.ucsc.edu> <46D6F71D.8050303@soe.ucsc.edu> Message-ID: <46D72733.1080205@soe.ucsc.edu> Hi again, Terry, We have a script that runs every night to add/drop tables to/from the rsync server (hgdownload). However, as a precaution, it has a limit on the number of tables it will delete per night. So, if a large number need to be deleted, it will only delete some that night, and then some more the next night, and the next, until all the tables are deleted. Presumably this is what happened to the requests to delete the 190 tables (chains and nets to mm8 from hg18 & rn4) on 8/28, then the request the next day to delete the tables of chains and nets to bosTau2 from hg18 & mm8 & rn4. There is probably a huge backlog of tables to delete. I'm not sure when it'll actually catch up, but at least we have an explanation now. Regards, Ann Zweig. Ann Zweig wrote: > Hello Terry, > > I'm the one who let you know you could drop those tables. And that was > correct. However, I see what you're saying -- they are still on hgdownload. I > will look into this today. > > Regards, > Ann Zweig. > > > > Terry Furey wrote: >> Hi Kayla - >> >> I appreciate the updates like this very much. Previously, I believe we >> were told that we could remove the mm8 chain and net tables from hg18 and >> rn4. I did this yesterday, and they >> >> Thanks, >> >> Terry >> >> On Wed, 29 Aug 2007, Kayla Smith wrote: >> >>> Good afternoon Mirror Sites: >>> >>> There are new chain and net tables to bosTau3, replacing the old ones to >>> bosTau2. It is safe to delete the following tables from the following >>> databases: >>> >>> hg18: >>> netBosTau2 >>> *chainBosTau2 >>> *chainBosTau2Link >>> >>> mm8: >>> netBosTau2 >>> *chainBosTau2 >>> *chainBosTau2Link >>> >>> rn4: >>> netBosTau2 >>> *chainBosTau2 >>> *chainBosTau2Link >>> >>> >>> Thanks, >>> >>> Kayla Smith >>> UCSC Genome Bioinformatics Group >>> _______________________________________________ >>> Genome-mirror mailing list >>> Genome-mirror at soe.ucsc.edu >>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>> >> _______________________________________________ >> Genome-mirror mailing list >> Genome-mirror at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From tsfurey at duke.edu Thu Aug 30 13:41:50 2007 From: tsfurey at duke.edu (Terry Furey) Date: Thu, 30 Aug 2007 16:41:50 -0400 (EDT) Subject: [Genome-mirror] some cow tables can be dropped In-Reply-To: <46D72733.1080205@soe.ucsc.edu> References: <46D5C6F8.9050806@cse.ucsc.edu> <46D6F71D.8050303@soe.ucsc.edu> <46D72733.1080205@soe.ucsc.edu> Message-ID: Hi Ann - Thanks for tracking this down. It sounds like I should just wait a couple of days for the backlog to take care of itself, and then try doing the deletions then and see what happens. Thanks! Terry On Thu, 30 Aug 2007, Ann Zweig wrote: > Hi again, Terry, > > We have a script that runs every night to add/drop tables to/from the > rsync server (hgdownload). However, as a precaution, it has a limit on the > number of tables it will delete per night. So, if a large number need to be > deleted, it will only delete some that night, and then some more the next > night, and the next, until all the tables are deleted. > > Presumably this is what happened to the requests to delete the 190 > tables (chains and nets to mm8 from hg18 & rn4) on 8/28, then the request the > next day to delete the tables of chains and nets to bosTau2 from hg18 & mm8 & > rn4. There is probably a huge backlog of tables to delete. I'm not sure > when it'll actually catch up, but at least we have an explanation now. > > Regards, > Ann Zweig. > > > > Ann Zweig wrote: >> Hello Terry, >> >> I'm the one who let you know you could drop those tables. And that >> was correct. However, I see what you're saying -- they are still on >> hgdownload. I will look into this today. >> >> Regards, >> Ann Zweig. >> >> >> >> Terry Furey wrote: >>> Hi Kayla - >>> >>> I appreciate the updates like this very much. Previously, I believe we >>> were told that we could remove the mm8 chain and net tables from hg18 and >>> rn4. I did this yesterday, and they >>> >>> Thanks, >>> >>> Terry >>> >>> On Wed, 29 Aug 2007, Kayla Smith wrote: >>> >>>> Good afternoon Mirror Sites: >>>> >>>> There are new chain and net tables to bosTau3, replacing the old ones to >>>> bosTau2. It is safe to delete the following tables from the following >>>> databases: >>>> >>>> hg18: >>>> netBosTau2 >>>> *chainBosTau2 >>>> *chainBosTau2Link >>>> >>>> mm8: >>>> netBosTau2 >>>> *chainBosTau2 >>>> *chainBosTau2Link >>>> >>>> rn4: >>>> netBosTau2 >>>> *chainBosTau2 >>>> *chainBosTau2Link >>>> >>>> >>>> Thanks, >>>> >>>> Kayla Smith >>>> UCSC Genome Bioinformatics Group >>>> _______________________________________________ >>>> Genome-mirror mailing list >>>> Genome-mirror at soe.ucsc.edu >>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>>> >>> _______________________________________________ >>> Genome-mirror mailing list >>> Genome-mirror at soe.ucsc.edu >>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >> _______________________________________________ >> Genome-mirror mailing list >> Genome-mirror at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > -- ---------------------------------------------------------------- Terrence S. Furey Scholar, Institute for Genome Sciences and Policy (IGSP) Assistant Research Professor Dept of Biostatistics and Bioinformatics Dept of Computer Science Duke University 101 Science Dr, Box 3382 Durham, NC 27708 Phone: 919-668-4728 Fax: 919-668-0795