From davide.cittaro at ifom-ieo-campus.it Fri May 2 06:41:26 2008 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Fri, 2 May 2008 15:41:26 +0200 Subject: [Genome-mirror] mirror versions and RSS Message-ID: Hi all, some GB versions have not been announced (I think the latest announced was v176), wouldn't it be nice to have a RSS feed for this page: http://genome-test.cse.ucsc.edu/builds/versions.html Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From hiram at soe.ucsc.edu Fri May 2 09:54:31 2008 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Fri, 02 May 2008 09:54:31 -0700 Subject: [Genome-mirror] mirror versions and RSS In-Reply-To: References: Message-ID: <481B4747.9000800@soe.ucsc.edu> Thanks for the suggestion Davide. We'll see if that is practical. We have been pretty consistent now for the past couple of years with a new release just about every two weeks, with an occasional miss once in a while. You can count on a release on a 2-week schedule. --Hiram Davide Cittaro wrote: > Hi all, some GB versions have not been announced (I think the latest > announced was v176), wouldn't it be nice to have a RSS feed for this > page: > > http://genome-test.cse.ucsc.edu/builds/versions.html > > Thanks > > d > > > /* > Davide Cittaro > > Cogentech - Consortium for Genomic Technologies > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303007 > e-mail: davide.cittaro at ifom-ieo-campus.it > */ > > > > _______________________________________________ > 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 May 2 16:45:06 2008 From: aamp at ucsc.edu (Andy Pohl) Date: Fri, 2 May 2008 16:45:06 -0700 Subject: [Genome-mirror] v181 Genome Browser Available Message-ID: <9fa943760805021645yce4eb1dg3b2d46ac5644a07c@mail.gmail.com> Hello, I guess it's been a while since the last announcement... sorry about that. The v181 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v181.zip cartDump cartReset das hgc hgBlat hgConvert hgCustom hgEncodeDataVersions hgGateway hgGene hgGenome hgLiftOver hgNear hgPcr hgSession hgTables 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 v181 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v181-preview and v181-final to see all the code and data changes in this release. Have a nice weekend! Andy Pohl UCSC CBSE From galt at soe.ucsc.edu Mon May 5 12:00:56 2008 From: galt at soe.ucsc.edu (Galt Barber) Date: Mon, 5 May 2008 12:00:56 -0700 (PDT) Subject: [Genome-mirror] [Genome] Question regarding mRNA seq In-Reply-To: References: Message-ID: You are right that if you click the page before the cgi finishes drawing it, it can show you data from a previous cart state. Thus you lookked at the 1485aa seq, then you clicked on the 915aa seq before the full page was drawn, and it showed you the value from the previous cart state. We will fix this very soon. Meanwhile, if you allow all of the hgGene page to finish drawing completely before clicking links on the page, this problem will not occur. Thanks very much for bringing this problem to our attention! -Galt On Mon, 5 May 2008, Bishwanath Chatterjee wrote: > Hi > I am going through the mouse genome browser to look for PCSK5 gene. This > gene as per literature have two isoform A and B. The A isoform supposed to > be 915 aa and B form should be 2087 aa. On This genome site it shows two > forms one with 915 aa and other with 1485aa. The 1485 is part of the isoform > B. But when you click one 915aa seq, it also shows you 1485. > > Also now UCSC browser shifted to their own nomenclature instead of > traditional Genbank accession. From Genbank accession, you can always go and > find the features of the cDNA. I am not sure how to find the link or if UCSC > browser have more details of the links from uc008gxp.1 .. > > Thanks > Bishwanath > Bishwanath Chatterjee, Ph. D. > Building 10 Room 6N240 > Laboratory of Developmental Biology > National Heart Lung and Blood Institute > National Institute of Health > Bethesda, MD 20892 > Tel 301-451-1672 > Fax 301-480-1808 > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From Janet_Yang at dfci.harvard.edu Tue May 6 08:08:11 2008 From: Janet_Yang at dfci.harvard.edu (Yang, Janet Q.) Date: Tue, 6 May 2008 11:08:11 -0400 Subject: [Genome-mirror] when I do need to update Genome Browser mirror site Message-ID: Dear Genome Browser staff, I have down loaded mirror site whole Genome Browser on our server now. I have heard that you will release a new version of the Genome Browser source code every two Weeks. My question is: 1). Can you tell me how often I need to update my Genome Browser on our server form your http://genome.ucsc.edu/admin/mirror.html website? 2). Do you have regular date for update mirror site Genome Browser? Can you tell me the date? So I will not miss the new version? Thank you very much! Janet Yang Dana farber Cancer Institute. Boston, Ma 02115 617-632-4283 (office phone) The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information. From rhead at soe.ucsc.edu Tue May 6 10:07:45 2008 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Tue, 06 May 2008 10:07:45 -0700 Subject: [Genome-mirror] when I do need to update Genome Browser mirror site In-Reply-To: References: Message-ID: <48209061.7030000@soe.ucsc.edu> Hello Janet, You are correct: we release a tested version of the source code approximately every other Friday (sometimes there are delays or schedule changes), and it is made available on http://hgdownload.cse.ucsc.edu/admin/ by the following Monday, if not sooner. The last release, v181, was made available Friday, May 2, and was announced on the genome-mirror mailing list: http://www.soe.ucsc.edu/pipermail/genome-mirror/2008-May/000778.html I recommend subscribing to the genome-mirror mailing list to receive update messages: http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror You can also browse and search previously answered questions on the mailing list here: http://genome.ucsc.edu/contacts.html#mirror -- Brooke Rhead UCSC Genome Bioinformatics Group Yang, Janet Q. wrote: > Dear Genome Browser staff, > > > > I have down loaded mirror site whole Genome Browser on our server now. > > I have heard that you will release a new version of the Genome Browser source > code every two > > Weeks. > > > > My question is: > > > > 1). Can you tell me how often I need to update my Genome Browser on our server > form your http://genome.ucsc.edu/admin/mirror.html website? > > > > 2). Do you have regular date for update mirror site Genome Browser? Can you tell > me the date? So I will not miss the new version? > > > > > > Thank you very much! > > > > Janet Yang > > > > Dana farber Cancer Institute. > > Boston, Ma 02115 > > 617-632-4283 (office phone) > > > > > > > The information transmitted in this electronic communication is intended only > for the person or entity to whom it is addressed and may contain confidential > and/or privileged material. Any review, retransmission, dissemination or other > use of or taking of any action in reliance upon this information by persons or > entities other than the intended recipient is prohibited. If you received this > information in error, please contact the Compliance HelpLine at 800-856-1983 and > properly dispose of this information. > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From Janet_Yang at dfci.harvard.edu Tue May 6 10:23:05 2008 From: Janet_Yang at dfci.harvard.edu (Yang, Janet Q.) Date: Tue, 6 May 2008 13:23:05 -0400 Subject: [Genome-mirror] when I do need to update Genome Browser mirror site In-Reply-To: <48209061.7030000@soe.ucsc.edu> Message-ID: Hi Brooke, Thank you so very much for all your help! Thanks, and Sincerely, Janet -----Original Message----- From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] Sent: Tuesday, May 06, 2008 1:08 PM To: Yang, Janet Q. Cc: genome-mirror at soe.ucsc.edu Subject: Re: [Genome-mirror] when I do need to update Genome Browser mirror site Hello Janet, You are correct: we release a tested version of the source code approximately every other Friday (sometimes there are delays or schedule changes), and it is made available on http://hgdownload.cse.ucsc.edu/admin/ by the following Monday, if not sooner. The last release, v181, was made available Friday, May 2, and was announced on the genome-mirror mailing list: http://www.soe.ucsc.edu/pipermail/genome-mirror/2008-May/000778.html I recommend subscribing to the genome-mirror mailing list to receive update messages: http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror You can also browse and search previously answered questions on the mailing list here: http://genome.ucsc.edu/contacts.html#mirror -- Brooke Rhead UCSC Genome Bioinformatics Group Yang, Janet Q. wrote: > Dear Genome Browser staff, > > > > I have down loaded mirror site whole Genome Browser on our server now. > > I have heard that you will release a new version of the Genome Browser source > code every two > > Weeks. > > > > My question is: > > > > 1). Can you tell me how often I need to update my Genome Browser on our server > form your http://genome.ucsc.edu/admin/mirror.html website? > > > > 2). Do you have regular date for update mirror site Genome Browser? Can you tell > me the date? So I will not miss the new version? > > > > > > Thank you very much! > > > > Janet Yang > > > > Dana farber Cancer Institute. > > Boston, Ma 02115 > > 617-632-4283 (office phone) > > > > > > > The information transmitted in this electronic communication is intended only > for the person or entity to whom it is addressed and may contain confidential > and/or privileged material. Any review, retransmission, dissemination or other > use of or taking of any action in reliance upon this information by persons or > entities other than the intended recipient is prohibited. If you received this > information in error, please contact the Compliance HelpLine at 800-856-1983 and > properly dispose of this information. > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From a.miotto at griffith.edu.au Thu May 8 17:00:23 2008 From: a.miotto at griffith.edu.au (Amanda Miotto) Date: Fri, 9 May 2008 10:00:23 +1000 Subject: [Genome-mirror] uploading custom onto the mirror Message-ID: I am trying to upload custom tracks onto the Griffith mirror using ucscMakeTracks.pl and have some queries. The tracks are going into the mysql database using hgLoadBed easily, and I have altered the my_tracks.ra file, created the necessary file in track_groups, and run ucscMakeTracks, with the output below, however the tracks are not appearing on the mirror. At first I assumed it was the method that I was writing my_tracks.ra but after borrowing a test bed file from QFAB and the data for my_tracks.ra as a positive control and the browser is still unchanged.The following is my output from ucscMakeTracks.pl -b $ ./ucscMakeTracks.pl -b ==> Loading tracks for my_tracks.ra Loaded 2 track descriptions total Loaded database custom_tracks ==> Loading tracks for /home/data/track_groups/1.0002+custom_tracks, +eG.ra Loaded 2 track descriptions total Loaded database custom_tracks ==> Loading tracks for /home/data/track_groups/1.001+a-person +esk.ra Loaded 2 track descriptions total Loaded database custom_tracks Any theories? Thank you! Amanda Miotto a.miotto at griffith.edu.au From ginger2 at u.washington.edu Thu May 8 16:15:55 2008 From: ginger2 at u.washington.edu (Ginger Cheng) Date: Thu, 08 May 2008 16:15:55 -0700 Subject: [Genome-mirror] wigColorBy using a 'bed 9' as reference? Message-ID: <482389AB.2050009@u.washington.edu> Hello, Browser Gurus, I'm intrigued by the wigColorBy function to customize the coloring of a wig track. Have used before with a very simple bed track as color reference. Wondering if it may work for a 'bed 9' track, as we can define the color of a 'bed 9' track freely using the 9th column of data table. Thank you for any hints ginger From hiram at soe.ucsc.edu Fri May 9 08:27:06 2008 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Fri, 09 May 2008 08:27:06 -0700 Subject: [Genome-mirror] uploading custom onto the mirror In-Reply-To: References: Message-ID: <48246D4A.30600@soe.ucsc.edu> Good Morning Amanda: This procedure you are using to load custom tracks is from another mirror site user. You'll have to get advice from them on how to do that. The method we recommend to load tracks is to use one of the track loaders, such as hgLoadBed, then add your track to a trackDb.ra file. See also, the file in the source tree: src/product/README.trackDb --Hiram Amanda Miotto wrote: > > I am trying to upload custom tracks onto the Griffith mirror using > ucscMakeTracks.pl and have some queries. > The tracks are going into the mysql database using hgLoadBed easily, and I > have altered the my_tracks.ra file, created the necessary file in > track_groups, and run ucscMakeTracks, with the output below, however the > tracks are not appearing on the mirror. At first I assumed it was the > method that I was writing my_tracks.ra but after borrowing a test bed file > from QFAB and the data for my_tracks.ra as a positive control and the > browser is still unchanged.The following is my output from > ucscMakeTracks.pl -b > > > $ ./ucscMakeTracks.pl -b > ==> Loading tracks for my_tracks.ra > Loaded 2 track descriptions total > Loaded database custom_tracks > ==> Loading tracks for /home/data/track_groups/1.0002+custom_tracks, > +eG.ra > Loaded 2 track descriptions total > Loaded database custom_tracks > ==> Loading tracks for /home/data/track_groups/1.001+a-person > +esk.ra > Loaded 2 track descriptions total > Loaded database custom_tracks > > > > Any theories? > Thank you! > > Amanda Miotto > a.miotto at griffith.edu.au From hiram at soe.ucsc.edu Fri May 9 09:44:42 2008 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Fri, 09 May 2008 09:44:42 -0700 Subject: [Genome-mirror] wigColorBy using a 'bed 9' as reference? In-Reply-To: <482389AB.2050009@u.washington.edu> References: <482389AB.2050009@u.washington.edu> Message-ID: <48247F7A.6070606@soe.ucsc.edu> Good Morning Ginger: I'm guessing you have tried this and I and think it doesn't work. Looking at the code, it seems to be able to color only via the trackDb specified 'color' and 'altColor', it doesn't look like it knows how to look for the color in column 9. This would have to be a feature request to make this work. We'll put it on our list of features to consider. --Hiram Ginger Cheng wrote: > Hello, Browser Gurus, > > I'm intrigued by the wigColorBy function to customize the coloring of a > wig track. Have used before with a very simple bed track as color > reference. Wondering if it may work for a 'bed 9' track, as we can > define the color of a 'bed 9' track freely using the 9th column of data > table. > > Thank you for any hints > > > ginger From amowjoodi at sickkids.ca Tue May 13 12:31:42 2008 From: amowjoodi at sickkids.ca (amowjoodi at sickkids.ca) Date: Tue, 13 May 2008 15:31:42 -0400 (EDT) Subject: [Genome-mirror] Mistake Message-ID: <3328.142.20.207.201.1210707102.squirrel@webmail.sickkids.ca> Hello Dear I think there is a spelling mistake in the UCSC Genome Browser web page. Please have a look at this paragraph: Genome Browser contacts: We maintain two public interactive mailing lists (genome at soe.ucsc.edu and genome-mirror at soe.ucsc.edu) where you can post specific questions about the UCSC Genome Browser software, database, genome assemblies, release cycles, amd mirroring. The mistake is: amd I think it is: and Best regards Ali From donnak at soe.ucsc.edu Tue May 13 13:42:26 2008 From: donnak at soe.ucsc.edu (Donna Karolchik) Date: Tue, 13 May 2008 13:42:26 -0700 Subject: [Genome-mirror] Mistake References: <3328.142.20.207.201.1210707102.squirrel@webmail.sickkids.ca> Message-ID: <044b01c8b539$e15b9ce0$0ba8a8c0@donnakLT> Thanks, Ali -- this will be fixed on our site this afternoon. -Donna ----------------------------------- Donna Karolchik Genome Browser Project Manager UCSC Genome Bioinformatics Group http://genome.ucsc.edu ----- Original Message ----- From: To: Cc: Sent: Tuesday, May 13, 2008 12:31 PM Subject: [Genome-mirror] Mistake > Hello Dear > I think there is a spelling mistake in the UCSC Genome Browser > web page. > Please have a look at this paragraph: > > Genome Browser contacts: > We maintain two public interactive mailing lists > (genome at soe.ucsc.edu and > genome-mirror at soe.ucsc.edu) where you can post specific > questions about > the UCSC Genome Browser software, database, genome assemblies, > release > cycles, amd mirroring. > > The mistake is: amd > I think it is: and > > Best regards > Ali > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From larrym at soe.ucsc.edu Fri May 16 13:45:40 2008 From: larrym at soe.ucsc.edu (Larry Meyer) Date: Fri, 16 May 2008 13:45:40 -0700 Subject: [Genome-mirror] v182 Genome Browser Available Message-ID: <20080516204540.GB15512@soe.ucsc.edu> Hello, The v182 source is now available at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v182.zip cartDump cartReset das hgc hgBlat hgConvert hgCustom hgGateway hgGene hgGenome hgLiftOver hgNear hgPcr hgSession hgTables hgTracks hgTrackUi hgVisiGene mkEncodeFrameset hgEncodeDataVersions pbGateway pbGlobal pbTracks phyloGif /usr/local/apache/cgi-bin/all.joiner /usr/local/apache/cgi-bin/galaAvail.tab /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 v182 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v182-preview and v182-final to see all the code and data changes in this release. Have a nice weekend! Larry Meyer UCSC CBSE From hooverdm at helix.nih.gov Mon May 19 10:14:18 2008 From: hooverdm at helix.nih.gov (David Hoover) Date: Mon, 19 May 2008 13:14:18 -0400 Subject: [Genome-mirror] cross site scripting Message-ID: <4831B56A.3000204@helix.nih.gov> We've found a vulnerability in our build of the Genome Browser that allows cross-site scripting (v1.1430 of hgTracks.c). The position field of the URL for hgTracks can substituted with javascript code. For example, the default URL for hg18 in hgTracks: http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=107472242&clade=vertebrate&org=Human&db=hg18&position=chrX%3A151%2C073%2C054-151%2C383%2C976&pix=620&Submit=submit&hgsid=107472242 can be modified with the javascript code "> so that http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=107472242&clade=vertebrate&org=Human&db=hg18&position="%3E%3Cscript%3Ealert("test")%3C%2Fscript%3E&pix=620&Submit=submit&hgsid=107472242 now displays a pop-up window. It could be made to do much worse, like steal cookies to falsify authentication and prompt a user to download browser plugins. I'm not sure if other Genome Browser executables are vulnerable or not, but you might want to check. Cheers, David Hoover, Helix Systems Staff From larrym at soe.ucsc.edu Mon May 19 13:29:19 2008 From: larrym at soe.ucsc.edu (Larry Meyer) Date: Mon, 19 May 2008 13:29:19 -0700 Subject: [Genome-mirror] cross site scripting In-Reply-To: <4831B56A.3000204@helix.nih.gov> References: <4831B56A.3000204@helix.nih.gov> Message-ID: <20080519202919.GC18872@soe.ucsc.edu> Hi David, Thanks for pointing this out and sending us a detailed description of the problem. We have fixed this by html escaping the appropriate output. This fix will be available in the next browser release (v183). We are also auditing our code to find similar problems. Thanks again, Larry Meyer UCSC Genome Browser On Mon, May 19, 2008 at 01:14:18PM -0400, David Hoover wrote: > We've found a vulnerability in our build of the Genome Browser that > allows cross-site scripting (v1.1430 of hgTracks.c). The position field > of the URL for hgTracks can substituted with javascript code. > > For example, the default URL for hg18 in hgTracks: > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=107472242&clade=vertebrate&org=Human&db=hg18&position=chrX%3A151%2C073%2C054-151%2C383%2C976&pix=620&Submit=submit&hgsid=107472242 > > can be modified with the javascript code > > "> > > so that > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=107472242&clade=vertebrate&org=Human&db=hg18&position="%3E%3Cscript%3Ealert("test")%3C%2Fscript%3E&pix=620&Submit=submit&hgsid=107472242 > > now displays a pop-up window. > > It could be made to do much worse, like steal cookies to falsify > authentication and prompt a user to download browser plugins. > > I'm not sure if other Genome Browser executables are vulnerable or not, > but you might want to check. > > Cheers, > David Hoover, Helix Systems Staff > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From mike at genocentrix.com Thu May 29 04:32:52 2008 From: mike at genocentrix.com (Michael Pheasant) Date: Thu, 29 May 2008 13:32:52 +0200 Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra Message-ID: <769b2fc30805290432n3c8d21dfpab20b91a01a84028@mail.gmail.com> Hi In the mirror we are working on in Australia we have tried to separate the mirrored files from the files the users can change. The mirrored files are all mounted read-only from the users perspective and so we can safely update the mirror and know that no user data gets overwritten. One of the users is trying to make custom tracks with microarray data and we have run into the problem that the microarrayGroups.ra config files reside in the cgi-bin/hgCgiData/ directory. The users cannot write to this directory so cannot create their own microarray tracks. We are looking at a workaround but just wanted to bring this scenario to your attention. Cheers Mike. From kuhn at soe.ucsc.edu Thu May 29 09:14:04 2008 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Thu, 29 May 2008 09:14:04 -0700 Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra Message-ID: <200805291614.JAA24263@moondance.cse.ucsc.edu> hello, mike, It happens that one of our engineers has just about completed implementing user-driven microarray custom tracks. they should be available in the next release two weeks from tomorrow (though please don't take that as a guarantee!). best wishes, --b0b kuhn ucsc genome bioinformatics group > From genome-mirror-bounces at soe.ucsc.edu Thu May 29 09:07:14 2008 > To: "genome mirror" > Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra > > Hi > > In the mirror we are working on in Australia we have tried to separate the > mirrored files from the files the users can change. The mirrored files are > all mounted read-only from the users perspective and so we can safely update > the mirror and know that no user data gets overwritten. > > One of the users is trying to make custom tracks with microarray data and we > have run into the problem that the microarrayGroups.ra config files reside > in the cgi-bin/hgCgiData/ directory. The users cannot write to this > directory so cannot create their own microarray tracks. > > We are looking at a workaround but just wanted to bring this scenario to > your attention. > > > Cheers > > Mike. > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From fanhsu at soe.ucsc.edu Thu May 29 09:24:32 2008 From: fanhsu at soe.ucsc.edu (Fan Hsu) Date: Thu, 29 May 2008 09:24:32 -0700 Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra In-Reply-To: <769b2fc30805290432n3c8d21dfpab20b91a01a84028@mail.gmail.com> References: <769b2fc30805290432n3c8d21dfpab20b91a01a84028@mail.gmail.com> Message-ID: <001901c8c1a8$7a1b5fe0$6b00a8c0@duo4t> Hi Michael, FYI, we are working on a new UCSC Cancer Genomics Browser project which has a similar need to support private user data and yet with full access to the public data. We have some tentative solution up and running. This may still be months (if not years) away from full public release. But if you are interested, please contact me directly to have further discussion. Fan. -----Original Message----- From: genome-mirror-bounces at soe.ucsc.edu [mailto:genome-mirror-bounces at soe.ucsc.edu] On Behalf Of Michael Pheasant Sent: Thursday, 29 May, 2008 4:33 AM To: genome mirror Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra Hi In the mirror we are working on in Australia we have tried to separate the mirrored files from the files the users can change. The mirrored files are all mounted read-only from the users perspective and so we can safely update the mirror and know that no user data gets overwritten. One of the users is trying to make custom tracks with microarray data and we have run into the problem that the microarrayGroups.ra config files reside in the cgi-bin/hgCgiData/ directory. The users cannot write to this directory so cannot create their own microarray tracks. We are looking at a workaround but just wanted to bring this scenario to your attention. Cheers Mike. _______________________________________________ Genome-mirror mailing list Genome-mirror at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From kuhn at soe.ucsc.edu Thu May 29 09:37:42 2008 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Thu, 29 May 2008 09:37:42 -0700 Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra Message-ID: <200805291637.JAA24890@moondance.cse.ucsc.edu> let me amend that. the new functionality is for maf tracks, not microarray tracks. microarray custom tracks have been around for some time. > From genome-mirror at soe.ucsc.edu Thu May 29 09:14:53 2008 > To: genome-mirror at soe.ucsc.edu, mike at genocentrix.com > Subject: Re: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra > > > hello, mike, > > It happens that one of our engineers has just about completed > implementing user-driven microarray custom tracks. they should > be available in the next release two weeks from tomorrow (though > please don't take that as a guarantee!). > > best wishes, > > --b0b kuhn > ucsc genome bioinformatics group > > > From genome-mirror-bounces at soe.ucsc.edu Thu May 29 09:07:14 2008 > > To: "genome mirror" > > Subject: [Genome-mirror] cgi-bin/hgCgiData/*/microarrayGroups.ra > > > > Hi > > > > In the mirror we are working on in Australia we have tried to separate the > > mirrored files from the files the users can change. The mirrored files are > > all mounted read-only from the users perspective and so we can safely update > > the mirror and know that no user data gets overwritten. > > > > One of the users is trying to make custom tracks with microarray data and we > > have run into the problem that the microarrayGroups.ra config files reside > > in the cgi-bin/hgCgiData/ directory. The users cannot write to this > > directory so cannot create their own microarray tracks. > > > > We are looking at a workaround but just wanted to bring this scenario to > > your attention. > > > > > > Cheers > > > > Mike. > > _______________________________________________ > > 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 James.Zhu at ARS.USDA.GOV Fri May 30 10:27:58 2008 From: James.Zhu at ARS.USDA.GOV (Zhu, James) Date: Fri, 30 May 2008 13:27:58 -0400 Subject: [Genome-mirror] Download errors Message-ID: <6B4AF69268EFAE4C80A786BA99F7A6670292B782@MD-MAIL-01.ARSNET.ARS.USDA.GOV> I excuted the following to download bosTau4 database. # rsync -avzP --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/bosTau4/database /var/www/html/godenPath/bosTau4/database Then I received the output as following: receiving file list ... 146 files to consider rsync: mkdir "/var/www/html/godenPath/bosTau4/database" failed: No such file or directory (2) rsync error: error in file IO (code 11) at main.c(381) What is wrong with it? James From rhead at soe.ucsc.edu Fri May 30 11:03:29 2008 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Fri, 30 May 2008 11:03:29 -0700 Subject: [Genome-mirror] Download errors In-Reply-To: <6B4AF69268EFAE4C80A786BA99F7A6670292B782@MD-MAIL-01.ARSNET.ARS.USDA.GOV> References: <6B4AF69268EFAE4C80A786BA99F7A6670292B782@MD-MAIL-01.ARSNET.ARS.USDA.GOV> Message-ID: <48404171.3070607@soe.ucsc.edu> Hi James, I think you have a typo in the pathname: "godenPath" should be "goldenPath". -- Brooke Rhead UCSC Genome Bioinformatics Group Zhu, James wrote: > I excuted the following to download bosTau4 database. > # rsync -avzP --delete --max-delete=20 > rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/bosTau4/database > /var/www/html/godenPath/bosTau4/database > > Then I received the output as following: > receiving file list ... > 146 files to consider > rsync: mkdir "/var/www/html/godenPath/bosTau4/database" failed: No such > file or directory (2) > rsync error: error in file IO (code 11) at main.c(381) > > What is wrong with it? > > James > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From kuhn at soe.ucsc.edu Fri May 30 11:27:36 2008 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Fri, 30 May 2008 11:27:36 -0700 Subject: [Genome-mirror] Download errors Message-ID: <200805301827.LAA29962@moondance.cse.ucsc.edu> dear James, there is a missing "l" in goldenPath in your file specification. best wishes, --b0b kuhn ucsc genome bioiinformatics group > From genome-mirror at soe.ucsc.edu Fri May 30 11:01:39 2008 > To: > Subject: [Genome-mirror] Download errors > > I excuted the following to download bosTau4 database. > # rsync -avzP --delete --max-delete=20 > rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/bosTau4/database > /var/www/html/godenPath/bosTau4/database > > Then I received the output as following: > receiving file list ... > 146 files to consider > rsync: mkdir "/var/www/html/godenPath/bosTau4/database" failed: No such > file or directory (2) > rsync error: error in file IO (code 11) at main.c(381) > > What is wrong with it? > > James > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > > 2008 > Return-Path: > X-Spam-Checker-Version: SpamAssassin 3.1.9 (2007-02-13) on lobo.cse.ucsc.edu > X-Spam-Level: > X-Spam-Status: No, score=-1.4 required=5.0 tests=ALL_TRUSTED,SPF_HELO_PASS > autolearn=unavailable version=3.1.9 > Received: from mailgw.soe.ucsc.edu (mailgw.cse.ucsc.edu [128.114.48.9]) > by services.cse.ucsc.edu (8.13.6/8.13.1) with ESMTP id m4UI3F2W021744 > (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=OK) > for ; Fri, 30 May 2008 11:03:15 -0700 (PDT) > X-ASG-Debug-ID: 1212170595-447001e00000-7IYQTc > X-Barracuda-URL: http://mailgw.cse.ucsc.edu:8000/cgi-bin/mark.cgi > Received: from moondance.cse.ucsc.edu (localhost [127.0.0.1]) > by mailgw.soe.ucsc.edu (Spam Firewall) with SMTP > id 311EF9325F9; Fri, 30 May 2008 11:03:15 -0700 (PDT) > Received: from moondance.cse.ucsc.edu (moondance.cse.ucsc.edu [128.114.49.1]) by mailgw.soe.ucsc.edu with SMTP id AZNlHODLEeXwBPxT; Fri, 30 May 2008 11:03:15 -0700 (PDT) > X-ASG-Whitelist: Client > Received: (from kuhn at localhost) by moondance.cse.ucsc.edu (8.6.10/8.6.12) id LAA29243; Fri, 30 May 2008 11:03:13 -0700 > Date: Fri, 30 May 2008 11:03:13 -0700 > X-Barracuda-BBL-IP: nil > From: Robert Kuhn > Message-Id: <200805301803.LAA29243 at moondance.cse.ucsc.edu> > To: hiram at soe.ucsc.edu, larrym at soe.ucsc.edu > X-ASG-Orig-Subj: Re: Fwd: something is wrong with the i386 blat > Subject: Re: Fwd: something is wrong with the i386 blat > Cc: kuhn at soe.ucsc.edu > X-Barracuda-Connect: moondance.cse.ucsc.edu[128.114.49.1] > X-Barracuda-Start-Time: 1212170595 > X-Barracuda-Virus-Scanned: by Barracuda Spam Firewall at soe.ucsc.edu > > > > we can wait til next week to announce. it is not uncommon > that we announce on monday or tuesday. is someone looking at > a fix for this issue? > > > From larrym at soe.ucsc.edu Fri May 30 10:52:47 2008 > > To: Hiram Clawson > > Cc: Robert Kuhn > > Subject: Re: Fwd: something is wrong with the i386 blat > > > > Once QA has finished testing the release > > on RR and I am ready to notify the mirrors that > > a release is now available, what do I do > > if we can't build the 32bit version? > > > > Can I just wait until we can get that built? (i.e. is > > it ok if we don't notify mirrors until next week?) > > > > Or alternatively, can I just notify them of the 64-bit > > release and say there is no 32-bit release this week? > > > > -larry > > > > On Fri, May 30, 2008 at 09:51:50AM -0700, Hiram Clawson wrote: > > > Here's the deal folks. We need to do one of the following: > > > > > > 1. downgrade the titan development system so it is compatible with > > > the KK nodes > > > 2. upgrade the KK nodes so they are compatible with the new titan > > > development system version > > > 3. forget about KK and turn the thing off. > > > > > > Personally I don't care which option is chosen, but one must > > > be chosen if we are to move forward. > > > > > > --Hiram > > > > > > Larry Meyer wrote: > > > >Yeah, mark, cluster-admin upgraded gcc on titan this weds (not sure why). > > > > > > > >So, all is not apparently well on titan. > > > > > > > >I ran doNewBranch32.csh last night, which runs ./buildUtils.csh > > > >on titan (I think hiram built them on weds too). > > > > > > > >Someone want to volunteer to look into this? (I don't know anything > > > >about blat and am busy doing other build stuff right now). > > > > > > > >-larry > > > > > > > >----- Forwarded message from Mark Diekhans ----- > > > > > > > >From: Mark Diekhans > > > >Date: Fri, 30 May 2008 09:32:20 -0700 > > > >To: Larry Meyer > > > >Subject: something is wrong with the i386 blat > > > >X-Mailer: VM 8.0.9 under Emacs 22.1.50.1 (x86_64-unknown-linux-gnu) > > > > > > > > > > > >-rwxrwxr-x 1 larrym protein 245908 May 29 17:06 /cluster/bin/i386/blat* > > > > > > > >/cluster/bin/i386/blat > > > >Floating exception > > > > > > > >they upgraded titan, maybe a broken compiler? > > > > > > > >----- End forwarded message ----- > > > > > > >