From tsfurey at duke.edu Fri Feb 2 05:37:37 2007 From: tsfurey at duke.edu (Terry Furey) Date: Fri, 2 Feb 2007 08:37:37 -0500 (EST) Subject: [Genome-mirror] blat servers Message-ID: Hi - For a while, now, my links to blat servers have been broken. I get errors like "Couldn't find host blat5. h_errno 1". I believe this is because previously in the blatServers table in hgcentral, the host was a complete name , I believe something like "blat12.soe.ucsc.edu" or something. With just "blat12" in there now, it assumes it is on the local network, and obviously isn't in my case. Does this make sense? Thanks, Terry From kuhn at soe.ucsc.edu Fri Feb 2 09:11:27 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Fri, 2 Feb 2007 09:11:27 -0800 Subject: [Genome-mirror] blat servers Message-ID: <200702021711.JAA04813@moondance.cse.ucsc.edu> Hi, Terry, We have not changed the format of the blatServers table. I do not recall =ever= seeing a complete path in there. I believe your problem must stem from some other source. best wishes, --b0b > From genome-mirror-bounces at soe.ucsc.edu Fri Feb 2 08:23:33 2007 > To: genome-mirror at soe.ucsc.edu > Subject: [Genome-mirror] blat servers > > Hi - > > For a while, now, my links to blat servers have been broken. I get errors > like "Couldn't find host blat5. h_errno 1". I believe this is because > previously in the blatServers table in hgcentral, the host was a complete > name , I believe something like "blat12.soe.ucsc.edu" or something. With > just "blat12" in there now, it assumes it is on the local network, and > obviously isn't in my case. > > Does this make sense? > > Thanks, > > Terry > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From hiram at soe.ucsc.edu Fri Feb 2 09:13:38 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Fri, 02 Feb 2007 09:13:38 -0800 Subject: [Genome-mirror] blat servers In-Reply-To: References: Message-ID: <45C37142.8090409@soe.ucsc.edu> That is correct Terry. We do this on purpose so mirror sites will understand that they will be using our resources as they change those addresses. --Hiram Terry Furey wrote: > Hi - > > For a while, now, my links to blat servers have been broken. I get errors > like "Couldn't find host blat5. h_errno 1". I believe this is because > previously in the blatServers table in hgcentral, the host was a complete > name , I believe something like "blat12.soe.ucsc.edu" or something. With > just "blat12" in there now, it assumes it is on the local network, and > obviously isn't in my case. > > Does this make sense? > > Thanks, > > Terry From tsfurey at duke.edu Fri Feb 2 13:40:38 2007 From: tsfurey at duke.edu (Terry Furey) Date: Fri, 2 Feb 2007 16:40:38 -0500 (EST) Subject: [Genome-mirror] blat servers In-Reply-To: <45C37142.8090409@soe.ucsc.edu> References: <45C37142.8090409@soe.ucsc.edu> Message-ID: Afraid I'm going to have to disagree with both of you. This previously did work, and it works on the other mirrors at Wisconsin and UCSF without there being a noticeable change in the web address i.e. if you run a blat search at UCSF, it never looks like it leaves that site, but I am almost positive Paul is not running a blat server there. This is how it used to work at my site. I did change servers recently and this might be the source of the problem, but I am tracing down that it is trying to resolve the ip address for "blat5." and can't. Had this been a full name, it could. I do believe that at some point in the blatServers table, there was more than just "blat5" in the host field for "hg17", for instance, and that the full name could be resolved properly. So, the structure of the table hasn't changed, but I believe the content has. Of course, I can't prove that. I'll keep looking. Terry On Fri, 2 Feb 2007, Hiram Clawson wrote: > That is correct Terry. We do this on purpose so mirror sites will understand > that they will be using our resources as they change those addresses. > > --Hiram > > Terry Furey wrote: >> Hi - >> >> For a while, now, my links to blat servers have been broken. I get errors >> like "Couldn't find host blat5. h_errno 1". I believe this is because >> previously in the blatServers table in hgcentral, the host was a complete >> name , I believe something like "blat12.soe.ucsc.edu" or something. With >> just "blat12" in there now, it assumes it is on the local network, and >> obviously isn't in my case. >> >> Does this make sense? >> >> Thanks, >> >> Terry > From kuhn at soe.ucsc.edu Fri Feb 2 13:59:44 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Fri, 2 Feb 2007 13:59:44 -0800 Subject: [Genome-mirror] blat servers Message-ID: <200702022159.NAA27118@moondance.cse.ucsc.edu> I found some notes from some old blat updates that show that in July, 2005, the table contents were just the blat number. I used the files with LOAD DATA LOCAL infile to add rows to the table. [kuhn at hgwdev blatServers]$ ls -lt *blat* [deleted newer files] -rw-rw-r-- 1 kuhn protein 48 Jul 20 2005 newDanRerblat [kuhn at hgwdev blatServers]$ cat newDanRerblat danRer3 blat2 17779 0 0 danRer3 blat2 17778 1 0 > From genome-mirror-bounces at soe.ucsc.edu Fri Feb 2 13:52:24 2007 > To: Hiram Clawson > Cc: genome-mirror at soe.ucsc.edu > Subject: Re: [Genome-mirror] blat servers > > Afraid I'm going to have to disagree with both of you. This previously > did work, and it works on the other mirrors at Wisconsin and UCSF without > there being a noticeable change in the web address i.e. if you run a blat > search at UCSF, it never looks like it leaves that site, but I am almost > positive Paul is not running a blat server there. This is how it used to > work at my site. > > I did change servers recently and this might be the source of the problem, > but I am tracing down that it is trying to resolve the ip address for > "blat5." and can't. Had this been a full name, it could. I do believe > that at some point in the blatServers table, there was more than just > "blat5" in the host field for "hg17", for instance, and that the full name > could be resolved properly. So, the structure of the table hasn't > changed, but I believe the content has. Of course, I can't prove that. > > I'll keep looking. > > Terry > > On Fri, 2 Feb 2007, Hiram Clawson wrote: > > > That is correct Terry. We do this on purpose so mirror sites will understand > > that they will be using our resources as they change those addresses. > > > > --Hiram > > > > Terry Furey wrote: > >> Hi - > >> > >> For a while, now, my links to blat servers have been broken. I get errors > >> like "Couldn't find host blat5. h_errno 1". I believe this is because > >> previously in the blatServers table in hgcentral, the host was a complete > >> name , I believe something like "blat12.soe.ucsc.edu" or something. With > >> just "blat12" in there now, it assumes it is on the local network, and > >> obviously isn't in my case. > >> > >> Does this make sense? > >> > >> Thanks, > >> > >> Terry > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From m.pheasant at imb.uq.edu.au Fri Feb 2 14:43:07 2007 From: m.pheasant at imb.uq.edu.au (Michael Pheasant) Date: Sat, 03 Feb 2007 08:43:07 +1000 Subject: [Genome-mirror] blat servers In-Reply-To: References: <45C37142.8090409@soe.ucsc.edu> Message-ID: Hi Terry, At our site we have to run an SQL query on hgcentral whenever it is updated as otherwise for us the blat servers dont resolve: UPDATE blatServers SET host=concat(host,'.cse.ucsc.edu.') WHERE INSTR(host, '.')=0 If you figure out how your site worked without changing this table, let me know, so we can try the same. One thing I can think of is if your /etc/resolve.conf had a search path for .cse.ucsc.edu so that it would try resolving eg, blat5 as blat5.cse.ucsc.edu Cheers, Mike > > Afraid I'm going to have to disagree with both of you. This previously > did work, and it works on the other mirrors at Wisconsin and UCSF without > there being a noticeable change in the web address i.e. if you run a blat > search at UCSF, it never looks like it leaves that site, but I am almost > positive Paul is not running a blat server there. This is how it used to > work at my site. > > I did change servers recently and this might be the source of the problem, > but I am tracing down that it is trying to resolve the ip address for > "blat5." and can't. Had this been a full name, it could. I do believe > that at some point in the blatServers table, there was more than just > "blat5" in the host field for "hg17", for instance, and that the full name > could be resolved properly. So, the structure of the table hasn't > changed, but I believe the content has. Of course, I can't prove that. > > I'll keep looking. > > Terry > > On Fri, 2 Feb 2007, Hiram Clawson wrote: > >> That is correct Terry. We do this on purpose so mirror sites will >>understand >> that they will be using our resources as they change those addresses. >> >> --Hiram >> >> Terry Furey wrote: >>> Hi - >>> >>> For a while, now, my links to blat servers have been broken. I get errors >>> like "Couldn't find host blat5. h_errno 1". I believe this is because >>> previously in the blatServers table in hgcentral, the host was a complete >>> name , I believe something like "blat12.soe.ucsc.edu" or something. With >>> just "blat12" in there now, it assumes it is on the local network, and >>> obviously isn't in my case. >>> >>> Does this make sense? >>> >>> Thanks, >>> >>> Terry >> > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror __________________________________ 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 pmckenna at fastmail.us Fri Feb 2 18:30:28 2007 From: pmckenna at fastmail.us (Paul Mc Kenna) Date: Fri, 02 Feb 2007 18:30:28 -0800 Subject: [Genome-mirror] blat servers In-Reply-To: References: <45C37142.8090409@soe.ucsc.edu> Message-ID: <45C3F3C4.7090503@fastmail.us> Hi Terry, I have also always updated the blatServers field this way: UPDATE blatServers SET host=concat(host,?.cse.ucsc.edu?); It has always been a necessary step for the time our mirror has been up (not too long). I also agree with Michael that the /etc/resolve.conf edit might be possible explanation for why things might have worked previously for you Paul Mc Kenna Michael Pheasant wrote: > Hi Terry, > > At our site we have to run an SQL query on hgcentral whenever it is updated as > otherwise for us the blat servers dont resolve: > > UPDATE blatServers SET host=concat(host,'.cse.ucsc.edu.') WHERE INSTR(host, > '.')=0 > > If you figure out how your site worked without changing this table, let me > know, so > we can try the same. One thing I can think of is if your /etc/resolve.conf had > a search path for .cse.ucsc.edu > so that it would try resolving eg, blat5 as blat5.cse.ucsc.edu > > Cheers, > > Mike > > > > From hartera at soe.ucsc.edu Sat Feb 3 04:55:43 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Sat, 3 Feb 2007 04:55:43 -0800 (PST) Subject: [Genome-mirror] v151 Genome Browser available Message-ID: v151 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v151.zip Please note that v151 includes a new CGI : hgGenome. cartDump cartReset das hgc hgBlat hgConvert hgCustom hgEncodeDataVersions hgGateway hgGene hgGenome hgLiftOver hgNear hgPcr 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/* Contents of v151 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v151-preview and v151-final to see all the code and data changes in this release. Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu _______________________________________________ Genome-mirror mailing list Genome-mirror at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From maximilianh at gmail.com Sat Feb 3 15:13:58 2007 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Sun, 4 Feb 2007 00:13:58 +0100 Subject: [Genome-mirror] blat servers In-Reply-To: <45C3F3C4.7090503@fastmail.us> References: <45C37142.8090409@soe.ucsc.edu> <45C3F3C4.7090503@fastmail.us> Message-ID: <76f031ae0702031513q61e0f12g1f8b607e9ef184e0@mail.gmail.com> The same here. I remember that after having figured that one out, I mentioned it on the wiki at the time: http://genomewiki.ucsc.edu/index.php/Browser_installation max -- maximilian haeussler, haeussle_at_iaf.cnrs-gif.fr CNRS Gif-sur-Yvette On 03/02/07, Paul Mc Kenna wrote: > Hi Terry, > > I have also always updated the blatServers field this way: > > UPDATE blatServers SET host=concat(host,'.cse.ucsc.edu'); > > It has always been a necessary step for the time our mirror has been up > (not too long). I also agree with Michael that the /etc/resolve.conf > edit might be possible explanation for why things might have worked > previously for you > > Paul Mc Kenna > > > > Michael Pheasant wrote: > > Hi Terry, > > > > At our site we have to run an SQL query on hgcentral whenever it is updated as > > otherwise for us the blat servers dont resolve: > > > > UPDATE blatServers SET host=concat(host,'.cse.ucsc.edu.') WHERE INSTR(host, > > '.')=0 > > > > If you figure out how your site worked without changing this table, let me > > know, so > > we can try the same. One thing I can think of is if your /etc/resolve.conf had > > a search path for .cse.ucsc.edu > > so that it would try resolving eg, blat5 as blat5.cse.ucsc.edu > > > > Cheers, > > > > Mike > > > > > > > > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From tsfurey at duke.edu Sun Feb 4 10:51:32 2007 From: tsfurey at duke.edu (Terry Furey) Date: Sun, 4 Feb 2007 13:51:32 -0500 (EST) Subject: [Genome-mirror] blat servers In-Reply-To: <45C3F3C4.7090503@fastmail.us> References: <45C37142.8090409@soe.ucsc.edu> <45C3F3C4.7090503@fastmail.us> Message-ID: Well, I guess I can't argue anymore. I never have done anything special with this table before, and I know it used to work. Possibly Jorge and/or Paul T. did something when they set it up for me, but who knows. Thanks for the advice on the work-around. Terry On Fri, 2 Feb 2007, Paul Mc Kenna wrote: > Hi Terry, > > I have also always updated the blatServers field this way: > > UPDATE blatServers SET host=concat(host,?.cse.ucsc.edu?); > > It has always been a necessary step for the time our mirror has been up (not > too long). I also agree with Michael that the /etc/resolve.conf edit might be > possible explanation for why things might have worked previously for you > > Paul Mc Kenna > > > > Michael Pheasant wrote: >> Hi Terry, >> >> At our site we have to run an SQL query on hgcentral whenever it is updated >> as otherwise for us the blat servers dont resolve: >> >> UPDATE blatServers SET host=concat(host,'.cse.ucsc.edu.') WHERE >> INSTR(host, '.')=0 >> >> If you figure out how your site worked without changing this table, let me >> know, so >> we can try the same. One thing I can think of is if your /etc/resolve.conf >> had a search path for .cse.ucsc.edu >> so that it would try resolving eg, blat5 as blat5.cse.ucsc.edu >> >> Cheers, >> >> Mike >> >> >> >> > > -- ---------------------------------------------------------------- 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 From elliott at nhgri.nih.gov Mon Feb 5 14:01:39 2007 From: elliott at nhgri.nih.gov (Elliott H Margulies) Date: Mon, 05 Feb 2007 17:01:39 -0500 Subject: [Genome-mirror] hgconf public mysql access Message-ID: <45C7A943.1000302@nhgri.nih.gov> Hello, I'm trying to setup the kent source tree tools to use the public mysql database instead of my internal database. I attempted this by changing the settings in my .hg.conf file, however I don't know how to configure this without a password. If I make it a null password that doesn't work and if I remove the password line from the .hg.conf file it says it's not properly formatted. Any ideas? Is this feasible? Regards, Elliott From rhead at soe.ucsc.edu Tue Feb 6 17:35:41 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Tue, 06 Feb 2007 17:35:41 -0800 Subject: [Genome-mirror] hgconf public mysql access In-Reply-To: <45C7A943.1000302@nhgri.nih.gov> References: <45C7A943.1000302@nhgri.nih.gov> Message-ID: <45C92CED.6060000@soe.ucsc.edu> Hello Elliott, We have created a user/password combination for you to put into your .hg.conf file, which I will send to you off-list. Please let us know if you run into any problems with this solution. -- Brooke Rhead UCSC Genome Bioinformatics Group Elliott H Margulies wrote: > Hello, > > I'm trying to setup the kent source tree tools to use the public mysql > database instead of my internal database. I attempted this by changing > the settings in my .hg.conf file, however I don't know how to configure > this without a password. If I make it a null password that doesn't work > and if I remove the password line from the .hg.conf file it says it's > not properly formatted. > > Any ideas? Is this feasible? > > Regards, > Elliott > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From davide.cittaro at ifom-ieo-campus.it Wed Feb 7 07:03:47 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 7 Feb 2007 16:03:47 +0100 Subject: [Genome-mirror] dp2 nib or 2bit? Message-ID: Hi, in order to set up a blat server for dp2, I wonder which files should I use: the 759 nib or dp2.2bit? Additionally, I've noticed that 2bit files reside in /gbdb/GENOME/ whereas .nib files in /gbdb/ GENOME/nib/... dp2.2bit is in /gbdb/dp2/nib/... Is this desired? d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ From hiram at soe.ucsc.edu Wed Feb 7 10:16:18 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Wed, 7 Feb 2007 10:16:18 -0800 Subject: [Genome-mirror] dp2 nib or 2bit? In-Reply-To: References: Message-ID: <44d0f89888f39e5e5ddaf6dfe7ace8f2@soe.ucsc.edu> Good Morning David: It depends upon what is in the chromInfo table for the assembly. It looks like it has the contig nib files in there, so you should use the nib directory. The presence of the dp2.2bit file in the nib directory looks like a very early mistake we made from 2004. Since the 2bit file isn't in the chromInfo file, it most likely is unused for anything. It should be in /gdbd/dp2/dp2.2bit as you have observed every other assembly. --Hiram On 2007 Feb 07, , at 7:03 AM, Davide Cittaro wrote: > Hi, in order to set up a blat server for dp2, I wonder which files > should I use: the 759 nib or dp2.2bit? Additionally, I've noticed > that 2bit files reside in /gbdb/GENOME/ whereas .nib files in /gbdb/ > GENOME/nib/... dp2.2bit is in /gbdb/dp2/nib/... Is this desired? > > d > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303355 > 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 galt at soe.ucsc.edu Wed Feb 7 10:16:25 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Wed, 7 Feb 2007 10:16:25 -0800 (PST) Subject: [Genome-mirror] dp2 nib or 2bit? In-Reply-To: References: Message-ID: Some (older) assemblies make the .2bit file in the nib/ subdirectory simply because that's where the nibs had always been and were used to putting it there. Later we realized that some assemblies might not need nibs at all for any step, and so the .2bit location was changed to just /gbdb/$GENOME instead of in the nib subdirectory. However assemblies that were already released were left as they were in this regard. It is usually better to use a .2bit for gfServer blat. -Galt On Wed, 7 Feb 2007, Davide Cittaro wrote: > Hi, in order to set up a blat server for dp2, I wonder which files > should I use: the 759 nib or dp2.2bit? Additionally, I've noticed > that 2bit files reside in /gbdb/GENOME/ whereas .nib files in /gbdb/ > GENOME/nib/... dp2.2bit is in /gbdb/dp2/nib/... Is this desired? > > d > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303355 > 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 kuhn at soe.ucsc.edu Fri Feb 9 11:13:20 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Fri, 9 Feb 2007 11:13:20 -0800 Subject: [Genome-mirror] dropped some hg17 tables Message-ID: <200702091913.LAA25413@moondance.cse.ucsc.edu> Dear mirrors: If you do not have automatic deletion of tables running on your rsyncs, you may wish to drop a set of tables that we recently removed from the hg17 assembly. they are 290 Mb and are no longer used. they had been part of an earlier Conservation track that has been replaced. the tables are: *netBlastz {chicken_netBlastz chimp_netBlastz dog_netBlastz fugu_netBlastz mouse_netBlastz rat_netBlastz zebrafish_netBlastz} best wishes, --b0b kuhn ucsc genome bioinformatics group From davide.cittaro at ifom-ieo-campus.it Wed Feb 21 02:43:01 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 21 Feb 2007 11:43:01 +0100 Subject: [Genome-mirror] question about new "session" feature Message-ID: Hi there, I've seen you announced a new feature: genome browser now supports sessions. I wonder when and if this feature will be available for mirroring and, also, if mirroring procedures page will be updated to include "session" instruction. I see that it is based on php, so I suppose one has to set up a local wiki (based on mediawiki?)... Since I perform rsync of htdocs every night, I also suppose that tomorrow I'll have a "session" link that simply doesn't work, am I right? Thanks Davide /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ From hiram at soe.ucsc.edu Wed Feb 21 08:02:44 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Wed, 21 Feb 2007 08:02:44 -0800 Subject: [Genome-mirror] question about new "session" feature In-Reply-To: References: Message-ID: Good Morning David: It probably already works. All you need to do is add the following to your hg.conf file: # wiki connection data wiki.host=genomewiki.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID It will use the genomewiki, you don't need your own wiki. --Hiram On 2007 Feb 21, , at 2:43 AM, Davide Cittaro wrote: > Hi there, I've seen you announced a new feature: genome browser now > supports sessions. > I wonder when and if this feature will be available for mirroring > and, also, if mirroring procedures page will be updated to include > "session" instruction. > I see that it is based on php, so I suppose one has to set up a local > wiki (based on mediawiki?)... > Since I perform rsync of htdocs every night, I also suppose that > tomorrow I'll have a "session" link that simply doesn't work, am I > right? > > Thanks > > Davide > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303355 > 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 davide.cittaro at ifom-ieo-campus.it Wed Feb 21 08:10:24 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 21 Feb 2007 17:10:24 +0100 Subject: [Genome-mirror] question about new "session" feature In-Reply-To: References: Message-ID: <48C00FE4-F4D0-4D98-B03D-38B9238FC9E2@ifom-ieo-campus.it> Hi Hiram, thanks for the answer, > > It will use the genomewiki, you don't need your own wiki. Ok, I hope it works. I see only now the hgSession binary in my cgi- bin directory :-) d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ From davide.cittaro at ifom-ieo-campus.it Wed Feb 21 08:41:58 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 21 Feb 2007 17:41:58 +0100 Subject: [Genome-mirror] question about new "session" feature In-Reply-To: <48C00FE4-F4D0-4D98-B03D-38B9238FC9E2@ifom-ieo-campus.it> References: <48C00FE4-F4D0-4D98-B03D-38B9238FC9E2@ifom-ieo-campus.it> Message-ID: <6B6E69A0-9BD7-47AD-BB06-C67FA7BDD78B@ifom-ieo-campus.it> It works. Is hgSession displayed (and enabled) only if wiki.* are set in hg.conf? d On Feb 21, 2007, at 5:10 PM, Davide Cittaro wrote: > Ok, I hope it works. I see only now the hgSession binary in my cgi- > bin directory :-) > > d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ From hiram at soe.ucsc.edu Wed Feb 21 09:20:33 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Wed, 21 Feb 2007 09:20:33 -0800 Subject: [Genome-mirror] question about new "session" feature In-Reply-To: <6B6E69A0-9BD7-47AD-BB06-C67FA7BDD78B@ifom-ieo-campus.it> References: <48C00FE4-F4D0-4D98-B03D-38B9238FC9E2@ifom-ieo-campus.it> <6B6E69A0-9BD7-47AD-BB06-C67FA7BDD78B@ifom-ieo-campus.it> Message-ID: <6bc373b523f6ee162600ccd6aa90317a@soe.ucsc.edu> Yes, that's what turns it on and off. The code has been there for a long time. Only recent tweaks have taken place. We already see several things we would like to improve as we begin to use it more. --Hiram On 2007 Feb 21, , at 8:41 AM, Davide Cittaro wrote: > It works. Is hgSession displayed (and enabled) only if wiki.* are set > in hg.conf? > > d > On Feb 21, 2007, at 5:10 PM, Davide Cittaro wrote: > >> Ok, I hope it works. I see only now the hgSession binary in my cgi- >> bin directory :-) >> >> d From davide.cittaro at ifom-ieo-campus.it Thu Feb 22 06:41:10 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Thu, 22 Feb 2007 15:41:10 +0100 Subject: [Genome-mirror] gbdb genbank question In-Reply-To: <44FE1CD5.7030403@soe.ucsc.edu> References: <44FBFC34.4050204@ifom-ieo-campus.it> <44FE1CD5.7030403@soe.ucsc.edu> Message-ID: Hello again On Sep 6, 2006, at 2:56 AM, Brooke Rhead wrote: > Hello Davide, > > You do still need to keep GB 152 and 153 around for now, if you > want the click-throughs for mRNA/genomic alignments to continue to > work. However, we do periodically go through our databases and > remove references to older GenBank releases, so that we can drop > older releases from the /gbdb area. The developer in charge of > doing this has offered to expedite the process if you are desperate > for space. I can let you know when this has been done. > After some months (and a couple of genbank releases), I would like to know if something has changed in genbank handles. After all I only have these db mirrored: cb1 ce2 ci2 danRer3 danRer4 dm2 dp3 go hg17 hg18 hg17encodedev hgFixed mm7 mm8 panTro1 panTro2 proteins040115 proteins040315 proteins040515 proteins050415 proteins051015 proteins060115 proteome rn3 rn4 rheMac2 sacCer1 strPur1 uniProt visiGene xenTro1 xenTro2 So I wonder if I can free some space deleting some old gb releases among: 21G /gbdb/genbank/data/processed/genbank.152.0 22G /gbdb/genbank/data/processed/genbank.153.0 23G /gbdb/genbank/data/processed/genbank.154.0 23G /gbdb/genbank/data/processed/genbank.155.0 16G /gbdb/genbank/data/processed/genbank.156.0 24G /gbdb/genbank/data/processed/genbank.157.0 24G /gbdb/genbank/data/processed/genbank.158.0 539M /gbdb/genbank/data/processed/refseq.20 505M /gbdb/genbank/data/processed/refseq.21 Thanks Davide > -- > Brooke Rhead > UCSC Genome Bioinformatics > > > Davide Cittaro wrote: >> Hi there, I see that /gbdb area contains genbank data. I see that >> genbank releases 152-155 are available and they need ~100Gb space. >> I wonder if I still need GB 152 (and 153) if I'm mirroring only >> the following subset of genomes: >> cb1 >> ce2 >> ci2 >> danRer3 >> danRer4 >> dm2 >> hg17 >> hg18 >> mm7 >> mm8 >> panTro1 >> panTro2 >> rheMac2 >> rn3 >> rn4 >> sacCer1 >> xenTro1 >> xenTro2 >> Thanks >> d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ From ann at soe.ucsc.edu Thu Feb 22 09:28:12 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Thu, 22 Feb 2007 09:28:12 -0800 Subject: [Genome-mirror] gbdb genbank question In-Reply-To: References: <44FBFC34.4050204@ifom-ieo-campus.it> <44FE1CD5.7030403@soe.ucsc.edu> Message-ID: <45DDD2AC.4010202@soe.ucsc.edu> Hi Davide, I have consulted our genbank guru and he says that you need to keep all of the genbank and refseq releases you listed below. However, I note that you can drop two of the proteins databases. proteins040115 (because you don't mirror hg15) proteins040515 (because you don't mirror mm5) This is from hgcentral: mysql> select * from gdbPdb order by proteomeDb; +----------+----------------+ | genomeDb | proteomeDb | +----------+----------------+ | hg15 | proteins040115 | | default | proteins040315 | | hg16 | proteins040315 | | rn2 | proteins040315 | | rn3 | proteins040315 | | mm5 | proteins040515 | | mm6 | proteins050415 | | hg17 | proteins050415 | | mm7 | proteins051015 | | hg18 | proteins060115 | | mm8 | proteins060115 | | rn4 | proteins060115 | +----------+----------------+ That will give you a little more room. We will try to announce on this list when there is a large set of data that it is safe to drop from the mirror sites. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Davide Cittaro wrote: > Hello again > On Sep 6, 2006, at 2:56 AM, Brooke Rhead wrote: > >> Hello Davide, >> >> You do still need to keep GB 152 and 153 around for now, if you >> want the click-throughs for mRNA/genomic alignments to continue to >> work. However, we do periodically go through our databases and >> remove references to older GenBank releases, so that we can drop >> older releases from the /gbdb area. The developer in charge of >> doing this has offered to expedite the process if you are desperate >> for space. I can let you know when this has been done. >> > > After some months (and a couple of genbank releases), I would like to > know if something has changed in genbank handles. > After all I only have these db mirrored: > > cb1 > ce2 > ci2 > danRer3 > danRer4 > dm2 > dp3 > go > hg17 > hg18 > hg17encodedev > hgFixed > mm7 > mm8 > panTro1 > panTro2 > proteins040115 > proteins040315 > proteins040515 > proteins050415 > proteins051015 > proteins060115 > proteome > rn3 > rn4 > rheMac2 > sacCer1 > strPur1 > uniProt > visiGene > xenTro1 > xenTro2 > > So I wonder if I can free some space deleting some old gb releases > among: > > 21G /gbdb/genbank/data/processed/genbank.152.0 > 22G /gbdb/genbank/data/processed/genbank.153.0 > 23G /gbdb/genbank/data/processed/genbank.154.0 > 23G /gbdb/genbank/data/processed/genbank.155.0 > 16G /gbdb/genbank/data/processed/genbank.156.0 > 24G /gbdb/genbank/data/processed/genbank.157.0 > 24G /gbdb/genbank/data/processed/genbank.158.0 > 539M /gbdb/genbank/data/processed/refseq.20 > 505M /gbdb/genbank/data/processed/refseq.21 > > Thanks > > Davide > >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics >> >> >> Davide Cittaro wrote: >>> Hi there, I see that /gbdb area contains genbank data. I see that >>> genbank releases 152-155 are available and they need ~100Gb space. >>> I wonder if I still need GB 152 (and 153) if I'm mirroring only >>> the following subset of genomes: >>> cb1 >>> ce2 >>> ci2 >>> danRer3 >>> danRer4 >>> dm2 >>> hg17 >>> hg18 >>> mm7 >>> mm8 >>> panTro1 >>> panTro2 >>> rheMac2 >>> rn3 >>> rn4 >>> sacCer1 >>> xenTro1 >>> xenTro2 >>> Thanks >>> d > > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303355 > 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 hiram at soe.ucsc.edu Thu Feb 22 09:37:24 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Thu, 22 Feb 2007 09:37:24 -0800 Subject: [Genome-mirror] rsync html files Message-ID: <45DDD4D4.10009@soe.ucsc.edu> Good Morning Mirror Site Operators: I just noticed that the rsync of the html hierarchy includes over 1,000 files in the admin/stats/ hierarchy. I'm assuming this is all useless junk for your purposes. Would anyone mind if I place that directory on the rsync exclude list at our end so you wouldn't be bothered by it ? --Hiram From m.pheasant at imb.uq.edu.au Thu Feb 22 10:06:27 2007 From: m.pheasant at imb.uq.edu.au (Michael Pheasant) Date: Fri, 23 Feb 2007 04:06:27 +1000 Subject: [Genome-mirror] rsync html files In-Reply-To: <45DDD4D4.10009@soe.ucsc.edu> References: <45DDD4D4.10009@soe.ucsc.edu> Message-ID: Hi Hiram I was going to ask you about this yesterday. The rsync target 'htdocs' (~15 Mb) has some files under WEBROOT that the rsync target 'genome' (>700Gb?) (also WEBROOT) does not have. - A lot of these are under admin/stats so if they can be deleted, then please do. Q: Could you make the rsync 'genome' target also mirror everything that 'htdocs' does? (It will only increase total size of 'genome' by a tiny fraction). For those of us with a full mirror, we could then do 'rsync --delete' on 'genome' to get all of WEBROOT, making sure that old files you delete get deleted off our mirror also, and we would not have to bother with 'htdocs'. Cheers, Mike. > Good Morning Mirror Site Operators: > > I just noticed that the rsync of the html hierarchy includes > over 1,000 files in the admin/stats/ hierarchy. I'm assuming > this is all useless junk for your purposes. Would anyone mind > if I place that directory on the rsync exclude list at our end > so you wouldn't be bothered by it ? > > --Hiram > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror __________________________________ 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 davide.cittaro at ifom-ieo-campus.it Thu Feb 22 12:33:53 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Thu, 22 Feb 2007 21:33:53 +0100 Subject: [Genome-mirror] gbdb genbank question In-Reply-To: <45DDD2AC.4010202@soe.ucsc.edu> References: <44FBFC34.4050204@ifom-ieo-campus.it> <44FE1CD5.7030403@soe.ucsc.edu> <45DDD2AC.4010202@soe.ucsc.edu> Message-ID: <342349CB-C5FD-4449-8B02-6B1D63C1BC3F@ifom-ieo-campus.it> Hi Ann On Feb 22, 2007, at 6:28 PM, Ann Zweig wrote: > > I have consulted our genbank guru and he says that you need to > keep all of the genbank and refseq releases you listed below. > Doh! > However, I note that you can drop two of the proteins databases. > > proteins040115 (because you don't mirror hg15) > proteins040515 (because you don't mirror mm5) Ok, sounds reasonable, thanks. d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ From ann at soe.ucsc.edu Fri Feb 23 10:06:08 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Fri, 23 Feb 2007 10:06:08 -0800 Subject: [Genome-mirror] rsync html files In-Reply-To: References: <45DDD4D4.10009@soe.ucsc.edu> Message-ID: <45DF2D10.9070709@soe.ucsc.edu> Hello Michael, We will examine our rsync exclude/include listings and see if the rsync can be arranged to do this. Regards, Ann Zweig. Michael Pheasant wrote: > Hi Hiram > > I was going to ask you about this yesterday. > The rsync target 'htdocs' (~15 Mb) has some files under WEBROOT > that the rsync target 'genome' (>700Gb?) (also WEBROOT) does not have. > - A lot of these are under admin/stats so if they can be deleted, then please > do. > > > Q: Could you make the rsync 'genome' target also mirror everything that > 'htdocs' does? > > (It will only increase total size of 'genome' by a tiny fraction). > For those of us with a full mirror, we could then do 'rsync --delete' on > 'genome' to get all of WEBROOT, > making sure that old files you delete get deleted off our mirror also, and we > would not have to bother with 'htdocs'. > > Cheers, > > Mike. > >> Good Morning Mirror Site Operators: >> >> I just noticed that the rsync of the html hierarchy includes >> over 1,000 files in the admin/stats/ hierarchy. I'm assuming >> this is all useless junk for your purposes. Would anyone mind >> if I place that directory on the rsync exclude list at our end >> so you wouldn't be bothered by it ? >> >> --Hiram >> _______________________________________________ >> Genome-mirror mailing list >> Genome-mirror at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > > __________________________________ > 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 mikem at informatics.jax.org Fri Feb 23 12:13:47 2007 From: mikem at informatics.jax.org (Mike McCrossin) Date: Fri, 23 Feb 2007 15:13:47 -0500 Subject: [Genome-mirror] Problem compiling source Message-ID: <45DF4AFB.7010605@informatics.jax.org> Hi, I'm trying to compile the source code on Solaris 8 running on a SPARC, and I run into error with undefined symbols. Below is an example of the make test in the jksrc/lib directory: make test cd tests && make test make[1]: Entering directory `/export/build/kent/src/lib/tests' gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_sparc -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I /usr/include -o errCatchTest.o -c errCatchTest.c mkdir -p output bin/sparc gcc -O -o bin/sparc/errCatchTest errCatchTest.o ../../lib/sparc/jkhgap.a ../../lib/sparc/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lm strip bin/sparc/errCatchTest bin/sparc/errCatchTest secret > output/errCatch.good diff expected/errCatch.good output/errCatch.good bin/sparc/errCatchTest bad > output/errCatch.bad diff expected/errCatch.bad output/errCatch.bad gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_sparc -Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I /usr/include -o htmlPageTest.o -c htmlPageTest.c gcc -O -o bin/sparc/htmlPageTest htmlPageTest.o ../../lib/sparc/jkhgap.a ../../lib/sparc/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lm Undefined first referenced symbol in file bind ../../lib/sparc/jkweb.a(net.o) accept ../../lib/sparc/jkweb.a(net.o) listen ../../lib/sparc/jkweb.a(net.o) gethostbyname ../../lib/sparc/jkweb.a(internet.o) socket ../../lib/sparc/jkweb.a(net.o) setsockopt ../../lib/sparc/jkweb.a(net.o) connect ../../lib/sparc/jkweb.a(net.o) inet_pton ../../lib/sparc/jkweb.a(internet.o) inet_ntop ../../lib/sparc/jkweb.a(internet.o) h_errno ../../lib/sparc/jkweb.a(internet.o) ld: fatal: Symbol referencing errors. No output written to bin/sparc/htmlPageTest collect2: ld returned 1 exit status make[1]: *** [htmlPageTest] Error 1 make[1]: Leaving directory `/export/build/kent/src/lib/tests' make: *** [test] Error 2 I appreciate any guidance you can give. Mike From hiram at soe.ucsc.edu Fri Feb 23 13:39:25 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Fri, 23 Feb 2007 13:39:25 -0800 Subject: [Genome-mirror] Problem compiling source In-Reply-To: <45DF4AFB.7010605@informatics.jax.org> References: <45DF4AFB.7010605@informatics.jax.org> Message-ID: <8feb31bcc7e249f4137fa5d79574e3cf@soe.ucsc.edu> Good Afternoon Mike: Try setting your MYSQLLIBS environment variable to: MYSQLLIBS=/your/path/to/libmysqlclient.a -lsocket -lnsl -lz Add the -lsocket -lnsl This should get you a proper compile and link. --Hiram On 2007 Feb 23, , at 12:13 PM, Mike McCrossin wrote: > Hi, > > I'm trying to compile the source code on Solaris 8 running on a > SPARC, > and I run into error with undefined symbols. Below is an example of > the > make test in the jksrc/lib directory: > > make test > cd tests && make test > make[1]: Entering directory `/export/build/kent/src/lib/tests' > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_sparc -Wformat -Wimplicit -Wuninitialized -Wreturn-type > -I../inc -I../../inc -I../../../inc -I../../../../inc > -I../../../../../inc -I /usr/include -o errCatchTest.o -c > errCatchTest.c > mkdir -p output bin/sparc > gcc -O -o bin/sparc/errCatchTest errCatchTest.o > ../../lib/sparc/jkhgap.a > ../../lib/sparc/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lm > strip bin/sparc/errCatchTest > bin/sparc/errCatchTest secret > output/errCatch.good > diff expected/errCatch.good output/errCatch.good > bin/sparc/errCatchTest bad > output/errCatch.bad > diff expected/errCatch.bad output/errCatch.bad > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_sparc -Wformat -Wimplicit -Wuninitialized -Wreturn-type > -I../inc -I../../inc -I../../../inc -I../../../../inc > -I../../../../../inc -I /usr/include -o htmlPageTest.o -c > htmlPageTest.c > gcc -O -o bin/sparc/htmlPageTest htmlPageTest.o > ../../lib/sparc/jkhgap.a > ../../lib/sparc/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lm > Undefined first referenced > symbol in file > bind ../../lib/sparc/jkweb.a(net.o) > accept ../../lib/sparc/jkweb.a(net.o) > listen ../../lib/sparc/jkweb.a(net.o) > gethostbyname ../../lib/sparc/jkweb.a(internet.o) > socket ../../lib/sparc/jkweb.a(net.o) > setsockopt ../../lib/sparc/jkweb.a(net.o) > connect ../../lib/sparc/jkweb.a(net.o) > inet_pton ../../lib/sparc/jkweb.a(internet.o) > inet_ntop ../../lib/sparc/jkweb.a(internet.o) > h_errno ../../lib/sparc/jkweb.a(internet.o) > ld: fatal: Symbol referencing errors. No output written to > bin/sparc/htmlPageTest > collect2: ld returned 1 exit status > make[1]: *** [htmlPageTest] Error 1 > make[1]: Leaving directory `/export/build/kent/src/lib/tests' > make: *** [test] Error 2 > > I appreciate any guidance you can give. > > > Mike > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From galt at soe.ucsc.edu Fri Feb 23 13:48:03 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Fri, 23 Feb 2007 13:48:03 -0800 (PST) Subject: [Genome-mirror] Problem compiling source In-Reply-To: <45DF4AFB.7010605@informatics.jax.org> References: <45DF4AFB.7010605@informatics.jax.org> Message-ID: Those symbols are all for network programming calls: bind accept listen gethostbyname socket setsockopt connect inet_pton inet_ntop h_errno solaris is not resolving these socket library calls. perhaps try adding -lsocket and maybe -lresolv for solaris so that the linker can find it. -Galt On Fri, 23 Feb 2007, Mike McCrossin wrote: > Hi, > > I'm trying to compile the source code on Solaris 8 running on a SPARC, > and I run into error with undefined symbols. Below is an example of the > make test in the jksrc/lib directory: > > make test > cd tests && make test > make[1]: Entering directory `/export/build/kent/src/lib/tests' > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_sparc -Wformat -Wimplicit -Wuninitialized -Wreturn-type > -I../inc -I../../inc -I../../../inc -I../../../../inc > -I../../../../../inc -I /usr/include -o errCatchTest.o -c errCatchTest.c > mkdir -p output bin/sparc > gcc -O -o bin/sparc/errCatchTest errCatchTest.o ../../lib/sparc/jkhgap.a > ../../lib/sparc/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lm > strip bin/sparc/errCatchTest > bin/sparc/errCatchTest secret > output/errCatch.good > diff expected/errCatch.good output/errCatch.good > bin/sparc/errCatchTest bad > output/errCatch.bad > diff expected/errCatch.bad output/errCatch.bad > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_sparc -Wformat -Wimplicit -Wuninitialized -Wreturn-type > -I../inc -I../../inc -I../../../inc -I../../../../inc > -I../../../../../inc -I /usr/include -o htmlPageTest.o -c htmlPageTest.c > gcc -O -o bin/sparc/htmlPageTest htmlPageTest.o ../../lib/sparc/jkhgap.a > ../../lib/sparc/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lm > Undefined first referenced > symbol in file > bind ../../lib/sparc/jkweb.a(net.o) > accept ../../lib/sparc/jkweb.a(net.o) > listen ../../lib/sparc/jkweb.a(net.o) > gethostbyname ../../lib/sparc/jkweb.a(internet.o) > socket ../../lib/sparc/jkweb.a(net.o) > setsockopt ../../lib/sparc/jkweb.a(net.o) > connect ../../lib/sparc/jkweb.a(net.o) > inet_pton ../../lib/sparc/jkweb.a(internet.o) > inet_ntop ../../lib/sparc/jkweb.a(internet.o) > h_errno ../../lib/sparc/jkweb.a(internet.o) > ld: fatal: Symbol referencing errors. No output written to > bin/sparc/htmlPageTest > collect2: ld returned 1 exit status > make[1]: *** [htmlPageTest] Error 1 > make[1]: Leaving directory `/export/build/kent/src/lib/tests' > make: *** [test] Error 2 > > I appreciate any guidance you can give. > > > Mike > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From barberan at biology.ucsc.edu Sat Feb 24 12:40:44 2007 From: barberan at biology.ucsc.edu (Sergio Barberan) Date: Sat, 24 Feb 2007 12:40:44 -0800 Subject: [Genome-mirror] C. elegans mirror Message-ID: <1172349644.5181.38.camel@elegans.ucsc.edu> Hi, I'm trying to install a mirror for the C. elegans genome, but I'm a little concern about the size of the "/gbdb data file area". If I just want to have the C. elegans genome do I really need to install this 400Gb?? Is there any other way around that? Thanks in advance for your help, Sergio Barberan From kayla at soe.ucsc.edu Mon Feb 26 14:38:37 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Mon, 26 Feb 2007 14:38:37 -0800 Subject: [Genome-mirror] C. elegans mirror In-Reply-To: <1172349644.5181.38.camel@elegans.ucsc.edu> References: <1172349644.5181.38.camel@elegans.ucsc.edu> Message-ID: <45E3616D.8050002@cse.ucsc.edu> Sergio, No, you don't need to install the whole /gbdb. Here is a previously answered mailinglist question on this topic: http://www.cse.ucsc.edu/pipermail/genome/2004-July/005105.html And here is the procedure for creating a mirror site: http://genome.ucsc.edu/admin/mirror.html See also these instructions for a minimal mirror site setup: http://genomewiki.ucsc.edu/index.php/Browser_installation I hope this is helpful to you. Please don't hesitate to contact us again if you require more assistance. Kayla Smith UCSC Genome Bioinformatics Group Sergio Barberan wrote: > Hi, > > I'm trying to install a mirror for the C. elegans genome, but I'm a > little concern about the size of the "/gbdb data file area". If I just > want to have the C. elegans genome do I really need to install this > 400Gb?? Is there any other way around that? > > Thanks in advance for your help, > Sergio Barberan > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From rhead at soe.ucsc.edu Mon Feb 26 15:57:25 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Mon, 26 Feb 2007 15:57:25 -0800 Subject: [Genome-mirror] Zebrafish (danRer1) assembly archived Message-ID: <45E373E5.1060206@soe.ucsc.edu> Hello Mirror Sites, We have archived the initial zebrafish assembly, danRer1 (Nov. 2003). It has been moved to http://genome-archive.cse.ucsc.edu/, and blat searches on danRer1 will no longer be supported. The danRer1 tables are ~6.9G in size including indices. The danRer1 tables have been removed from the main website (except for the 'chromInfo' table -- see below). The /gbdb/danRer1/* files will NOT be removed from our site. These files will be used by the archive server. They will also be used by the main website to continue to support liftOver from danRer1 to danRer2, and to supply data for other organisms' nets and chains that still point to danRer1 (the xenTro1 nets and chains still go to danRer1). To maintain an exact mirror of the UCSC site, DO NOT DELETE the /gbdb/danRer1/* files. Remove all of the tables from the danRer1 database EXCEPT for 'chromInfo' (this table is needed to maintain support for xenTro1 net and chain alignments). Edit hgcentral as follows: (1) remove the reference to danRer1 from the 'blatServers' table, and (2) keep the reference to 'danRer1' in dbDb, but set active=0. Mysql commands for hgcentral: delete from blatServers where db='danRer1'; update dbDb set active=0 where name='danRer1'; A new hgcentral.sql file including these changes will also be available after the code release scheduled for Friday, 2-23-2007. The .sql file will be released the following week. Alternatively, if you would like to save space and remove the /gbdb/danRer1/* files, it is safe to do so. The only difference you will see is a lack of alignment links for danRer1 nets and chains on the xenTro1 database. If you decide to remove /gbdb/danRer1/*, it is also safe to remove the entire danRer1 database, including 'chromInfo'. If you have any questions, please email us at genome-mirror at soe.ucsc.edu. -- Brooke Rhead UCSC Genome Bioinformatics Group From rhead at soe.ucsc.edu Mon Feb 26 16:39:26 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Mon, 26 Feb 2007 16:39:26 -0800 Subject: [Genome-mirror] Zebrafish (danRer1) assembly archived In-Reply-To: <45E373E5.1060206@soe.ucsc.edu> References: <45E373E5.1060206@soe.ucsc.edu> Message-ID: <45E37DBE.1040308@soe.ucsc.edu> Note: The next code release is scheduled for Friday, 3-2-2007 (not 2-23-07). -- Brooke Rhead UCSC Genome Bioinformatics Group Brooke Rhead wrote: > Hello Mirror Sites, > > We have archived the initial zebrafish assembly, danRer1 (Nov. > 2003). It has been moved to http://genome-archive.cse.ucsc.edu/, and > blat searches on danRer1 will no longer be supported. > > The danRer1 tables are ~6.9G in size including indices. The danRer1 > tables have been removed from the main website (except for the > 'chromInfo' table -- see below). > > The /gbdb/danRer1/* files will NOT be removed from our site. These > files will be used by the archive server. They will also be used by the > main website to continue to support liftOver from danRer1 to danRer2, > and to supply data for other organisms' nets and chains that still point > to danRer1 (the xenTro1 nets and chains still go to danRer1). > > To maintain an exact mirror of the UCSC site, DO NOT DELETE the > /gbdb/danRer1/* files. Remove all of the tables from the danRer1 > database EXCEPT for 'chromInfo' (this table is needed to maintain > support for xenTro1 net and chain alignments). Edit hgcentral as > follows: (1) remove the reference to danRer1 from the 'blatServers' > table, and (2) keep the reference to 'danRer1' in dbDb, but set active=0. > > Mysql commands for hgcentral: > > delete from blatServers where db='danRer1'; > update dbDb set active=0 where name='danRer1'; > > A new hgcentral.sql file including these changes will also be available > after the code release scheduled for Friday, 2-23-2007. The .sql file > will be released the following week. > > Alternatively, if you would like to save space and remove the > /gbdb/danRer1/* files, it is safe to do so. The only difference you will > see is a lack of alignment links for danRer1 nets and chains on the > xenTro1 database. If you decide to remove /gbdb/danRer1/*, it is also > safe to remove the entire danRer1 database, including 'chromInfo'. > > If you have any questions, please email us at genome-mirror at soe.ucsc.edu. > > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror