From franck at good.ibl.fr Fri Jun 1 02:48:14 2007 From: franck at good.ibl.fr (Franck De Graeve) Date: Fri, 01 Jun 2007 11:48:14 +0200 Subject: [Genome-mirror] expRatio Message-ID: <465FEB5E.9010804@good.ibl.fr> Hi all, I want add a track type expRatio in my local mirror, configuration in * * *hg17 : trackDb:* z_test_ratio Test _ratio expRatio Test 0 0 0 0 0 0 0 0 0 0 0 test 1 expDrawExons on expScale 3.0 expStep 0.5 expTable z_test2MedianExps groupings z_test2Groups *hgFixed table: *z_test2All, z_test2AllExps, z_test2AllRatio, z_test2Median, z_test2MedianExps, z_test2MedianRatio. I have a message : z_test2Groups not found Please help me. -- -. .-. .-. .-. .-. .-. .-. .-. .-. ||/|||\ /|||\|||\ /|||\|||\ /|||\|||\ /|||\ |/ \|||\|||/ \|||\|||/ \|||\|||/ \|||\|||/ ' `-' `-' `-' `-' `-' `-' `-' `-' franck at good.ibl.fr CNRS UMR 8090 - http://www-good.ibl.fr G?nomique et physiologie mol?culaire des maladies m?taboliques I.B.L - 1 rue du Pr Calmette, B.P.245, 59019 Lille Cedex Tel : 33 (0)3.20.87.10.71 Fax : 33 (0)3.20.87.10.31 ------------------------------------------------------------------- From ann at soe.ucsc.edu Fri Jun 1 12:22:33 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Fri, 01 Jun 2007 12:22:33 -0700 Subject: [Genome-mirror] expRatio In-Reply-To: <465FEB5E.9010804@good.ibl.fr> References: <465FEB5E.9010804@good.ibl.fr> Message-ID: <466071F9.5020501@cse.ucsc.edu> Hello Franck, It looks like there is something missing with your trackDb 'groupings' setting. Perhaps you are missing your associated microarrayGroups.ra files? Here is a complete discussion of creating a track of type expRatio: http://genomewiki.cse.ucsc.edu/index.php/Microarray_track Please have a look at that and write back if you still have questions. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Franck De Graeve wrote: > Hi all, > > I want add a track type expRatio in my local mirror, > configuration in * > * > > *hg17 : > trackDb:* > > z_test_ratio Test _ratio expRatio Test 0 0 0 0 0 0 > 0 0 0 0 0 test 1 expDrawExons on > expScale 3.0 > expStep 0.5 > expTable z_test2MedianExps > groupings z_test2Groups > > > *hgFixed > > table: > *z_test2All, z_test2AllExps, z_test2AllRatio, z_test2Median, > z_test2MedianExps, z_test2MedianRatio. > > I have a message : z_test2Groups not found > Please help me. > From galt at soe.ucsc.edu Fri Jun 1 13:16:27 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Fri, 1 Jun 2007 13:16:27 -0700 (PDT) Subject: [Genome-mirror] relative URLs Message-ID: People have occasionally asked us if we support relative URLs, particular scenarios where the user does not have access to the "ROOT" "/" of the webserver. For instance, they may have control only of things at or below their own subdirectory: http://someserver.com/~someuser/ http://someserver.com/~someuser/cgi-bin/ etc. Recently we have gone through the cgi source code and tried to change absolute URLs to relative URLs. We think we have found most of the changes required, but we could use some help testing. If anybody would like to try it and give us some feedback, that would be great. Thanks very much! Galt Barber Genome Browser staff UCSC From galt at soe.ucsc.edu Fri Jun 1 13:18:09 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Fri, 1 Jun 2007 13:18:09 -0700 (PDT) Subject: [Genome-mirror] relative URLs In-Reply-To: References: Message-ID: This actually won't be in the official release until v160 is out but you can obtain the latest cvs source by following the usual instructions and leaving out the "-rbeta" in the cvs command. -Galt On Fri, 1 Jun 2007, Galt Barber wrote: > > People have occasionally asked us if we support > relative URLs, particular scenarios where > the user does not have access to the "ROOT" "/" > of the webserver. > > For instance, they may have control only of things > at or below their own subdirectory: > > http://someserver.com/~someuser/ > http://someserver.com/~someuser/cgi-bin/ > etc. > > Recently we have gone through the cgi source code > and tried to change absolute URLs to relative URLs. > We think we have found most of the changes required, > but we could use some help testing. > > If anybody would like to try it and > give us some feedback, that would be great. > > Thanks very much! > > Galt Barber > > Genome Browser staff > UCSC > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > From aamp at ucsc.edu Mon Jun 4 12:40:44 2007 From: aamp at ucsc.edu (Andy Pohl) Date: Mon, 4 Jun 2007 12:40:44 -0700 Subject: [Genome-mirror] v160 browser available Message-ID: <9fa943760706041240i66e21ff9r28cb6bf4f7776efb@mail.gmail.com> Hello, v160 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v160.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/* Contents of v160 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v160-preview and v160-final to see all the code and data changes in this release. Have a nice week, Andy Pohl UCSC CBSE From aamp at ucsc.edu Mon Jun 4 14:05:43 2007 From: aamp at ucsc.edu (Andy Pohl) Date: Mon, 4 Jun 2007 14:05:43 -0700 Subject: [Genome-mirror] v160 browser available In-Reply-To: <9fa943760706041240i66e21ff9r28cb6bf4f7776efb@mail.gmail.com> References: <9fa943760706041240i66e21ff9r28cb6bf4f7776efb@mail.gmail.com> Message-ID: <9fa943760706041405k3fd3db54h3de3507f0c0379d9@mail.gmail.com> Hi again, There's a new cgi-bin directory with new data I forgot to mention: /usr/local/apache/cgi-bin/visiGeneData/* Please mirror that directory in addition so visiGene works properly. I apologize for the inconvenience. Andy Pohl UCSC CBSE On 6/4/07, Andy Pohl wrote: > Hello, > > v160 source is at: > http://hgdownload.cse.ucsc.edu/admin/jksrc.zip > > or labeled with source number: > http://hgdownload.cse.ucsc.edu/admin/jksrc.v160.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/* > > Contents of v160 may be seen at: > > http://genome-test.cse.ucsc.edu/builds/versions.html > > Please check both v160-preview and v160-final to see all the code > and data changes in this release. Have a nice week, > > Andy Pohl > UCSC CBSE > From davide.cittaro at ifom-ieo-campus.it Wed Jun 6 02:26:17 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 6 Jun 2007 11:26:17 +0200 Subject: [Genome-mirror] apache configuration In-Reply-To: <465DB300.1020107@soe.ucsc.edu> References: <925334A0-6DF5-40FD-A54E-2F3080F79E99@ifom-ieo-campus.it> <465DB300.1020107@soe.ucsc.edu> Message-ID: Hi Hiram On May 30, 2007, at 7:23 PM, Hiram Clawson wrote: > > Good Morning Davide: > > I do not notice any other special configurations we have on. > However, depending upon your Apache version, you could have > a variety of other parameters set. We operate a fairly ancient > version 1.3.34 - we don't require much from Apache and do > not need newer features. > I see... this is tough to debug. I've seen that *every* hg binary uses Set-Cookie header so I don't understand why apache fails in parsing it as I check the reordering option. I'm looking around but seems that there's no valuable documentation on this :-( I'm going to make some additional checks and, in case, be prepared to answer a lot of questions :-) 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)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From davide.cittaro at ifom-ieo-campus.it Wed Jun 6 07:54:12 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 6 Jun 2007 16:54:12 +0200 Subject: [Genome-mirror] hgTracks bug? Message-ID: Hi genome people. In order to understand why my local mirror has problems in reordering tracks (configure page) I found out that there is no header problem, simply hgTracks crashes as I check the reordering option. Apparently this was only reproducible via command line setting the hgsid parameter too (without it everything works fine, but it doesn't really matter now). The problem is that given: int a, *b; if ( *b == a) do something else do something else on Linux, OS X and Solaris it does something, on FreeBSD it crashes... I started a gdb session and found out that in hgTracks.c there are many loops and functions on tracks that have group member pointing to 0 (you say NULL). So, on my FreeBSD machine, this leads to a core dump: float dif = a->group->priority - b->group->priority; as a->group points to 0x0... After a long session I've seen that: 12836 if (hashFindVal(hash, groupName)!=NULL) 12837 { 12838 track->groupName = cloneString(groupName); 12839 track->group = hashFindVal(hash, groupName); 12840 } if hashFindVal(hash, groupName) equals to 0 I go into the code and so track->group is set to zero. After this there is no track->group- >priority for comparison made after 275 int tgCmpPriority(const void *va, const void *vb) 276 /* Compare to sort based on priority. */ 277 { 278 const struct track *a = *((struct track **)va); 279 const struct track *b = *((struct track **)vb); 280 float dif = a->group->priority - b->group->priority; and (as I wrote before) a->group->priority makes hgTracks crash. To patch my local version I had two ways, one is this: --- hgTracks.c Wed Jun 6 15:50:05 2007 +++ hgTracks.c.orig Fri May 25 22:03:38 2007 @@ -12836,7 +12836,7 @@ if (hashFindVal(hash, groupName)!=NULL) { track->groupName = cloneString(groupName); -// track->group = hashFindVal(hash, groupName); + track->group = hashFindVal(hash, groupName); } } /* Sort tracks by combined group/track priority, and and the other is this: --- hgTracks.c Wed Jun 6 16:14:53 2007 +++ hgTracks.c.orig Fri May 25 22:03:38 2007 @@ -12833,13 +12833,11 @@ groupName = cartUsualString(cart, cartVar, track->group- >name); if (sameString(groupName, track->group->name)) cartRemove(cart, cartVar); -/* if (hashFindVal(hash, groupName)!=NULL) { track->groupName = cloneString(groupName); track->group = hashFindVal(hash, groupName); } -*/ } /* Sort tracks by combined group/track priority, and * then add references to track to group. */ In one case I've commented out track->group reassignment, in the other I've commented out the entire "if" block. Actually the browser seems to work in both cases (I can't tell if it is working fine, I'm just responsible for its maintenance), but I have no idea which is the best solution and why that block is there, I haven't time to understand what hashFindVal, groupTracks and other functions do. Since I don't expect you to rewrite hgTracks code, I just would like to know what is that function for so that I can write a better patch. Cheers d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare 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 Wed Jun 6 16:36:55 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Wed, 06 Jun 2007 16:36:55 -0700 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: References: Message-ID: <46674517.80401@soe.ucsc.edu> Good Afternoon Davide: The code you mentioned: > 12836 if (hashFindVal(hash, groupName)!=NULL) > 12837 { > 12838 track->groupName = cloneString(groupName); > 12839 track->group = hashFindVal(hash, groupName); > 12840 } > > if hashFindVal(hash, groupName) equals to 0 I go into the code and so > track->group is set to zero. After this there is no track->group- > >priority for comparison made after Prevents any groupName from being added to the track->group item if it returns a NULL from the hashFindVal(). This assignment shouldn't be the source of the NULL's in your track group list. I suspect they must be getting in there from somewhere else. Can you check and verify your grp table on the various systems is the same in all cases ? Or at least appears to be sane. This processing loop is working on any group names coming in from your cart, or the group name from the track, and checking to see if those names exist as are found in the grp table. Any groups not found in grp should have been assigned to the "unknown" group in the loop just above this one. --Hiram Davide Cittaro wrote: > Hi genome people. In order to understand why my local mirror has > problems in reordering tracks (configure page) I found out that there > is no header problem, simply hgTracks crashes as I check the > reordering option. Apparently this was only reproducible via command > line setting the hgsid parameter too (without it everything works > fine, but it doesn't really matter now). > The problem is that given: > > int a, *b; > > if ( *b == a) > do something > else > do something else > on Linux, OS X and Solaris it does something, on FreeBSD it crashes... > > I started a gdb session and found out that in hgTracks.c there are > many loops and functions on tracks that have group member pointing to > 0 (you say NULL). So, on my FreeBSD machine, this leads to a core dump: > > float dif = a->group->priority - b->group->priority; > > as a->group points to 0x0... > After a long session I've seen that: > > 12836 if (hashFindVal(hash, groupName)!=NULL) > 12837 { > 12838 track->groupName = cloneString(groupName); > 12839 track->group = hashFindVal(hash, groupName); > 12840 } > > if hashFindVal(hash, groupName) equals to 0 I go into the code and so > track->group is set to zero. After this there is no track->group- > >priority for comparison made after > > 275 int tgCmpPriority(const void *va, const void *vb) > 276 /* Compare to sort based on priority. */ > 277 { > 278 const struct track *a = *((struct track **)va); > 279 const struct track *b = *((struct track **)vb); > 280 float dif = a->group->priority - b->group->priority; > > and (as I wrote before) a->group->priority makes hgTracks crash. To > patch my local version I had two ways, one is this: > > --- hgTracks.c Wed Jun 6 15:50:05 2007 > +++ hgTracks.c.orig Fri May 25 22:03:38 2007 > @@ -12836,7 +12836,7 @@ > if (hashFindVal(hash, groupName)!=NULL) > { > track->groupName = cloneString(groupName); > -// track->group = hashFindVal(hash, groupName); > + track->group = hashFindVal(hash, groupName); > } > } > /* Sort tracks by combined group/track priority, and > > and the other is this: > > --- hgTracks.c Wed Jun 6 16:14:53 2007 > +++ hgTracks.c.orig Fri May 25 22:03:38 2007 > @@ -12833,13 +12833,11 @@ > groupName = cartUsualString(cart, cartVar, track->group- > >name); > if (sameString(groupName, track->group->name)) > cartRemove(cart, cartVar); > -/* > if (hashFindVal(hash, groupName)!=NULL) > { > track->groupName = cloneString(groupName); > track->group = hashFindVal(hash, groupName); > } > -*/ > } > /* Sort tracks by combined group/track priority, and > * then add references to track to group. */ > > In one case I've commented out track->group reassignment, in the > other I've commented out the entire "if" block. > Actually the browser seems to work in both cases (I can't tell if it > is working fine, I'm just responsible for its maintenance), but I > have no idea which is the best solution and why that block is there, > I haven't time to understand what hashFindVal, groupTracks and other > functions do. Since I don't expect you to rewrite hgTracks code, I > just would like to know what is that function for so that I can write > a better patch. > > Cheers > > d > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303007 > e-mail: davide.cittaro at ifom-ieo-campus.it > */ From davide.cittaro at ifom-ieo-campus.it Thu Jun 7 00:42:53 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Thu, 7 Jun 2007 09:42:53 +0200 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: <46674517.80401@soe.ucsc.edu> References: <46674517.80401@soe.ucsc.edu> Message-ID: Hi Hiram On Jun 7, 2007, at 1:36 AM, Hiram Clawson wrote: > Can you check and verify > your grp table on the various systems is the same in all cases ? > Or at > least appears to be sane. Thanks for the hint. I've checked grp table on all databases here and it doesn't differ at all with the one you have there... After all I rsync tables every night. Is there another reason why I have some track->group = 0x0? d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From forgetta at gmail.com Thu Jun 7 12:05:08 2007 From: forgetta at gmail.com (Vince Forgetta) Date: Thu, 7 Jun 2007 15:05:08 -0400 Subject: [Genome-mirror] Make my own Chain, Net and LiftOver -- Path of least resistance Message-ID: Hi Guys and Gals, I am attempting to generate chain, net and liftOver files for my bacterial genome builds. What would be the most straightforward way to accomplish this? I read through the wiki and tried to run the two scripts, makeLoChain-align.csh or doSameSpeciesLiftOver.pl, but ran into problems with paths (no /cluster) and cluster queuing. Is there a way to bypass the alignment step and feed in an alignment file later in the process? Thank for the help. Vince P.S. If necessary, I wouldn't mind writing some code to help out in the "bypassing". From hiram at soe.ucsc.edu Thu Jun 7 16:11:47 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Thu, 07 Jun 2007 16:11:47 -0700 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: References: <46674517.80401@soe.ucsc.edu> Message-ID: <466890B3.5020905@soe.ucsc.edu> Good Afternoon Davide: I don't know why you would have a track->group of zero. Put in a debug printout of all the tracks as they are read in groupTracks() after they are set up: struct grp* grps = hLoadGrps(); during their first processing: for (grp = grps; grp != NULL; grp = grp->next) The zero should show up there ? The list is being added to with: AllocVar(group); slAddHead(&list, group); and filled in: hashAdd(hash, grp->name, group); group->name = cloneString(grp->name); group->label = cloneString(grp->label); --Hiram Davide Cittaro wrote: > Hi Hiram > On Jun 7, 2007, at 1:36 AM, Hiram Clawson wrote: > >> Can you check and verify >> your grp table on the various systems is the same in all cases ? >> Or at >> least appears to be sane. > > Thanks for the hint. I've checked grp table on all databases here and > it doesn't differ at all with the one you have there... After all I > rsync tables every night. Is there another reason why I have some > track->group = 0x0? > > d > > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > 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 rhead at soe.ucsc.edu Thu Jun 7 16:47:24 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Thu, 07 Jun 2007 16:47:24 -0700 Subject: [Genome-mirror] Make my own Chain, Net and LiftOver -- Path of least resistance In-Reply-To: References: Message-ID: <4668990C.1010703@soe.ucsc.edu> Hi Vince, Thanks for looking through the wiki first! As you can see, the scripts for making nets and chains were definitely developed with our specific environment in mind, but one of our developers has this advice for you: --- If he can modify the hardcoded paths in HgAutomate.pm and doSameSpeciesLiftOver.pl to local equivalents, then he should be able to run doSameSpeciesLiftOver.pl -debug locally to see what kind of scripts it dumps out. 'doSameSpeciesLiftOver.pl -continue net' might work if he can provide his own chained alignments. --- I hope this helps. Please let us know if you have further questions. -- Brooke Rhead UCSC Genome Bioinformatics Group Vince Forgetta wrote: > Hi Guys and Gals, > > > I am attempting to generate chain, net and liftOver files for my bacterial > genome builds. What would be the most straightforward way to accomplish > this? I read through the wiki and tried to run the two scripts, > makeLoChain-align.csh or doSameSpeciesLiftOver.pl, but ran into problems > with paths (no /cluster) and cluster queuing. Is there a way to bypass the > alignment step and feed in an alignment file later in the process? > > Thank for the help. > > Vince > > P.S. If necessary, I wouldn't mind writing some code to help out in the > "bypassing". > _______________________________________________ > 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 Fri Jun 8 01:20:30 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Fri, 8 Jun 2007 10:20:30 +0200 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: <466890B3.5020905@soe.ucsc.edu> References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> Message-ID: <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> Hi again, On Jun 8, 2007, at 1:11 AM, Hiram Clawson wrote: > > Put in a debug printout of all the tracks as they are read in > groupTracks() after they are set up: > struct grp* grps = hLoadGrps(); > during their first processing: > for (grp = grps; grp != NULL; grp = grp->next) > > The zero should show up there ? The list is being > added to with: > AllocVar(group); > slAddHead(&list, group); > > and filled in: > hashAdd(hash, grp->name, group); > group->name = cloneString(grp->name); > group->label = cloneString(grp->label); Actually, the first element of pTrackList makes all this crash (and other elements too if I allow a "jump", but let's stay on the first). Before line 12836 12836 if (hashFindVal(hash, groupName)!=NULL) 12837 { 12838 track->groupName = cloneString(groupName); 12839 track->group = hashFindVal(hash, groupName); 12840 } I have this first track: p *track $22 = {next = 0x9ab7600, mapName = 0x9a81310 "ct_CC", visibility = tvDense, limitedVis = tvHide, limitedVisSet = 0, longLabel = 0x98b6ce0 "CC_RARE", shortLabel = 0x98b6cd0 "CC", mapsSelf = 0 '\0', drawName = 0 '\0', colorShades = 0x0, color = {r = 0 '\0', g = 0 '\0', b = 0 '\0'}, ixColor = 0 '\0', altColorShades = 0x0, altColor = {r = 127 '\177', g = 127 '\177', b = 127 '\177'}, ixAltColor = 0 '\0', loadItems = 0x8061c60 , items = 0x0, itemName = 0x804b90c , mapItemName = 0x8061de0 , totalHeight = 0x804ace0 , height = 0, lineHeight = 10, heightPer = 9, itemHeight = 0x804a8a4 , drawItems = 0x804e7b8 , drawItemAt = 0x804cf50 , itemStart = 0x804edfc , itemEnd = 0x804ee08 , freeItems = 0x804b958 , itemColor = 0, itemNameColor = 0x804ccc4 , itemLabelColor = 0, mapItem = 0, hasUi = 1, extraUiData = 0x9a81330, trackFilter = 0, customPt = 0x942e580, customInt = 0, subType = 0, minRange = 0, maxRange = 0, scaleRange = 0, bedSize = 12, otherDb = 0x0, private = 0, priority = 10, defaultPriority = 10, groupName = 0x98b6d30 "user", group = 0x9aba0e0, defaultGroupName = 0x0, canPack = 1, ss = 0x0, tdb = 0x942e600, expScale = 0, expTable = 0x0, exonArrows = 1, exonArrowsAlways = 0, nextItemButtonable = 1, labelNextItemButtonable = 0, itemAttrTbl = 0x0, labelColor = 0 '\0', drawLeftLabels = 0, subtracks = 0x0, nextPrevItem = 0x804b9d0 , labelNextPrevItem = 0x804bd74 , loadTime = 0, drawTime = 0} and its group p *track->group $24 = {next = 0x9aba100, name = 0x9a81380 "user", label = 0x9a81390 "Custom Tracks", priority = 1, defaultPriority = 1, trackList = 0x0} This means to me that the track, its group and whatever else is loaded correctly and works fine. After the "if" block, I have p *track $25 = {next = 0x9ab7600, mapName = 0x9a81310 "ct_CC", visibility = tvDense, limitedVis = tvHide, limitedVisSet = 0, longLabel = 0x98b6ce0 "CC_RARE", shortLabel = 0x98b6cd0 "CC", mapsSelf = 0 '\0', drawName = 0 '\0', colorShades = 0x0, color = {r = 0 '\0', g = 0 '\0', b = 0 '\0'}, ixColor = 0 '\0', altColorShades = 0x0, altColor = {r = 127 '\177', g = 127 '\177', b = 127 '\177'}, ixAltColor = 0 '\0', loadItems = 0x8061c60 , items = 0x0, itemName = 0x804b90c , mapItemName = 0x8061de0 , totalHeight = 0x804ace0 , height = 0, lineHeight = 10, heightPer = 9, itemHeight = 0x804a8a4 , drawItems = 0x804e7b8 , drawItemAt = 0x804cf50 , itemStart = 0x804edfc , itemEnd = 0x804ee08 , freeItems = 0x804b958 , itemColor = 0, itemNameColor = 0x804ccc4 , itemLabelColor = 0, mapItem = 0, hasUi = 1, extraUiData = 0x9a81330, trackFilter = 0, customPt = 0x942e580, customInt = 0, subType = 0, minRange = 0, maxRange = 0, scaleRange = 0, bedSize = 12, otherDb = 0x0, private = 0, priority = 10, defaultPriority = 10, groupName = 0x8f847b0 "", group = 0x0, defaultGroupName = 0x0, canPack = 1, ss = 0x0, tdb = 0x942e600, expScale = 0, expTable = 0x0, exonArrows = 1, exonArrowsAlways = 0, nextItemButtonable = 1, labelNextItemButtonable = 0, itemAttrTbl = 0x0, labelColor = 0 '\0', drawLeftLabels = 0, subtracks = 0x0, nextPrevItem = 0x804b9d0 , labelNextPrevItem = 0x804bd74 , loadTime = 0, drawTime = 0} and, of course p *track->group Error accessing memory address 0x0: Bad address. HTH d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From maximilianh at gmail.com Fri Jun 8 05:17:37 2007 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Fri, 8 Jun 2007 13:17:37 +0100 Subject: [Genome-mirror] Make my own Chain, Net and LiftOver -- Path of least resistance In-Reply-To: <4668990C.1010703@soe.ucsc.edu> References: <4668990C.1010703@soe.ucsc.edu> Message-ID: <76f031ae0706080517j56f31813k7e89ad20b4a8107a@mail.gmail.com> Hi Vince, I'm having exactly the same problem and started a page on the genomewiki a week ago. http://genomewiki.cse.ucsc.edu/index.php/Whole_genome_alignment_howto This won't really help you but as we're exactly in the same situation perhaps we can share what worked. I've already run into problems at the first step (blastz) because my job is running since a week (I don't have a cluster, but really shouldn't need one for ~150 MB) as there are a several thousand scaffolds. I've asked Hiram on this and he replied: -- We break up both the query and the target sequence into about 10 million base chunks each, with 10,000 overlap on the target pieces, then lift the results back to chrom pieces. It is even more tricky for these scaffold based organisms. When you have a large query scaffold, and a tiny target scaffold, the run-time ironically increases to days per job. You can kinda cheat by creating a chrUn for the target, but this makes chains that span multiple scaffolds which is not correct. -- I've started with a script as simple as this: ------ basedir=/heap/ci/genome-jgi2/indiv compdir=/heap/cs/cs2/reftigs BLASTZPARAMS="H=2000 Y=3400 L=6000 K=2200" for i in $basedir/*; do blastz $i /heap/cs/cs2/cioSav2.fa $BLASTZPARAMS >> ci2-cs2.lav done ------ If you know a better alternative (hiram pointed out that pooling scaffolds is not a much better idea either and if I blastz each scaffold onto each other, I have to do 35 000 000 blastz invocations which is probably not a lot faster). Anyways, I appreciate any discussions/hints/questions... max On 08/06/07, Brooke Rhead wrote: > Hi Vince, > > Thanks for looking through the wiki first! As you can see, the scripts > for making nets and chains were definitely developed with our specific > environment in mind, but one of our developers has this advice for you: > > --- > If he can modify the hardcoded paths in HgAutomate.pm and > doSameSpeciesLiftOver.pl to local equivalents, then he should be able > to run doSameSpeciesLiftOver.pl -debug locally to see what kind of > scripts it dumps out. > > 'doSameSpeciesLiftOver.pl -continue net' might work if he can provide > his own chained alignments. > --- > > I hope this helps. Please let us know if you have further questions. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > Vince Forgetta wrote: > > Hi Guys and Gals, > > > > > > I am attempting to generate chain, net and liftOver files for my bacterial > > genome builds. What would be the most straightforward way to accomplish > > this? I read through the wiki and tried to run the two scripts, > > makeLoChain-align.csh or doSameSpeciesLiftOver.pl, but ran into problems > > with paths (no /cluster) and cluster queuing. Is there a way to bypass the > > alignment step and feed in an alignment file later in the process? > > > > Thank for the help. > > > > Vince > > > > P.S. If necessary, I wouldn't mind writing some code to help out in the > > "bypassing". > > _______________________________________________ > > 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 > -- Maximilian Haeussler, skype: maximilianhaeussler From maximilianh at gmail.com Fri Jun 8 05:33:16 2007 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Fri, 8 Jun 2007 13:33:16 +0100 Subject: [Genome-mirror] poor man's cluster Message-ID: <76f031ae0706080533w398a5fd4t606e4a593e834377@mail.gmail.com> Hi, the following is a strange idea but I want to check at least if anyone has ever tried something like this: You might have come across things like the patched x86 kernels from colinux.org, the vmware player or xen. Two years ago I was using windows xp running colinux (debian) with the ucsc source tree. It was working well and very fast (colinux: native speed, vmware was a quite slower). (to Davide: perhaps better than on Freebsd ;-) I don't have money for my own cluster, I don't really need one anyways :-), but there are so many powerful windows machines on this campus used by secretaries and doing nothing really useful: I wonder if anyone of you has ever tried a parasol (or e.g. condor)-based cluster with windows machines and an emulated linux on them? But perhaps it wouldn't make sense, since disk access should be quite slow over the network (whereas it is not used at night). If not: with the vmware player it would be at least quite easy to create a usb stick with the human genome browser on it... though, I agree, not as useful :-) ... cheers, Max From tsfurey at duke.edu Fri Jun 8 07:21:43 2007 From: tsfurey at duke.edu (Terry Furey) Date: Fri, 8 Jun 2007 10:21:43 -0400 (EDT) Subject: [Genome-mirror] hgcentral database Message-ID: Hi - I was just checking through my mirror and noticed that horse and platypus were not showing up as options. I checked, and I believe I have the full databases for these and the corresponding gbdb directories. What I tracked down was that they are currently not listed in the dbDb table in the hgcentral database, so they don't appear in the menu. I manually checked that I was updating the hgcentral database properly. Could you check and see if this table does need updating? It's still possible I'm missing something, but I can't figure out what. Thanks, Terry From ann at soe.ucsc.edu Fri Jun 8 10:31:18 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Fri, 08 Jun 2007 10:31:18 -0700 Subject: [Genome-mirror] hgcentral database In-Reply-To: References: Message-ID: <46699266.5020106@cse.ucsc.edu> Hi Terry, Our fault. We forgot to push that file with the CGI release last Friday. It's all up-to-date now. Sorry for the inconvenience. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Terry Furey wrote: > Hi - > > I was just checking through my mirror and noticed that horse and platypus > were not showing up as options. I checked, and I believe I have the full > databases for these and the corresponding gbdb directories. What I > tracked down was that they are currently not listed in the dbDb table in > the hgcentral database, so they don't appear in the menu. I manually > checked that I was updating the hgcentral database properly. > > Could you check and see if this table does need updating? It's still > possible I'm missing something, but I can't figure out what. > > Thanks, > > Terry > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From forgetta at gmail.com Fri Jun 8 13:36:52 2007 From: forgetta at gmail.com (Vincenzo Forgetta) Date: Fri, 08 Jun 2007 16:36:52 -0400 Subject: [Genome-mirror] Make my own Chain, Net and LiftOver -- Path of least resistance In-Reply-To: <76f031ae0706080517j56f31813k7e89ad20b4a8107a@mail.gmail.com> References: <4668990C.1010703@soe.ucsc.edu> <76f031ae0706080517j56f31813k7e89ad20b4a8107a@mail.gmail.com> Message-ID: <4669BDE4.1020209@gmail.com> Hi all, Got my liftover files! Turns out it was easier to follow the instructions in jksrc/kent/src/hg/doc/liftOver.txt. My genomes are ~4Mb so I don't need any of the automation stuff included in the perl scripts ... I just need to know the sequence of unix commands and ucsc utilities to run. Does anyone know how I can convert the chain/net files into a browser track (like the pairwise comparisons for human vs mouse, human vs chimp, etc). I tried using chainToAxt, then axtToBed, but my genomes are in 2bit format, not in per chr nib files. As a result chainToAxt complains: $ chainToAxt -bed chr_random.chain cdqaa0.2bit ../cdqaa1/cdqaa1.2bit stdout Can't open ../cdqaa1/cdqaa1.2bit/chr_random.nib to read: Not a directory Do I need to make nib files of the chromosomes ... which is acceptable as well. Thanks for all the help. Vince Maximilian Haeussler wrote: > Hi Vince, > > I'm having exactly the same problem and started a page on the > genomewiki a week ago. > http://genomewiki.cse.ucsc.edu/index.php/Whole_genome_alignment_howto > > This won't really help you but as we're exactly in the same situation > perhaps we can share what worked. > I've already run into problems at the first step (blastz) because my > job is running since a week (I don't have a cluster, but really > shouldn't need one for ~150 MB) as there are a several thousand > scaffolds. I've asked Hiram on this and he replied: > -- > We break up both the query and the > target sequence into about 10 million base chunks each, > with 10,000 overlap on the target pieces, then lift the results > back to chrom pieces. It is even more tricky for these scaffold > based organisms. When you have a large query scaffold, > and a tiny target scaffold, the run-time ironically increases > to days per job. You can kinda cheat by creating a chrUn > for the target, but this makes chains that span multiple > scaffolds which is not correct. > -- > > I've started with a script as simple as this: > ------ > basedir=/heap/ci/genome-jgi2/indiv > compdir=/heap/cs/cs2/reftigs > BLASTZPARAMS="H=2000 Y=3400 L=6000 K=2200" > > for i in $basedir/*; do > blastz $i /heap/cs/cs2/cioSav2.fa $BLASTZPARAMS >> ci2-cs2.lav > done > ------ > > If you know a better alternative (hiram pointed out that pooling > scaffolds is not a much better idea either and if I blastz each > scaffold onto each other, I have to do 35 000 000 blastz invocations > which is probably not a lot faster). Anyways, I appreciate any > discussions/hints/questions... > > max > On 08/06/07, Brooke Rhead wrote: >> Hi Vince, >> >> Thanks for looking through the wiki first! As you can see, the scripts >> for making nets and chains were definitely developed with our specific >> environment in mind, but one of our developers has this advice for you: >> >> --- >> If he can modify the hardcoded paths in HgAutomate.pm and >> doSameSpeciesLiftOver.pl to local equivalents, then he should be able >> to run doSameSpeciesLiftOver.pl -debug locally to see what kind of >> scripts it dumps out. >> >> 'doSameSpeciesLiftOver.pl -continue net' might work if he can provide >> his own chained alignments. >> --- >> >> I hope this helps. Please let us know if you have further questions. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> Vince Forgetta wrote: >> > Hi Guys and Gals, >> > >> > >> > I am attempting to generate chain, net and liftOver files for my >> bacterial >> > genome builds. What would be the most straightforward way to >> accomplish >> > this? I read through the wiki and tried to run the two scripts, >> > makeLoChain-align.csh or doSameSpeciesLiftOver.pl, but ran into >> problems >> > with paths (no /cluster) and cluster queuing. Is there a way to >> bypass the >> > alignment step and feed in an alignment file later in the process? >> > >> > Thank for the help. >> > >> > Vince >> > >> > P.S. If necessary, I wouldn't mind writing some code to help out in >> the >> > "bypassing". >> > _______________________________________________ >> > 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 Fri Jun 8 13:58:31 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Fri, 08 Jun 2007 13:58:31 -0700 Subject: [Genome-mirror] Make my own Chain, Net and LiftOver -- Path of least resistance In-Reply-To: <4669BDE4.1020209@gmail.com> References: <4668990C.1010703@soe.ucsc.edu> <76f031ae0706080517j56f31813k7e89ad20b4a8107a@mail.gmail.com> <4669BDE4.1020209@gmail.com> Message-ID: <4669C2F7.8010702@cse.ucsc.edu> Hi Vince, Maybe this wiki page would be helpful to you: http://genomewiki.cse.ucsc.edu/index.php/Conservation_Track Regards, Ann Zweig. Vincenzo Forgetta wrote: > Hi all, > > Got my liftover files! Turns out it was easier to follow the > instructions in jksrc/kent/src/hg/doc/liftOver.txt. My genomes are ~4Mb > so I don't need any of the automation stuff included in the perl scripts > ... I just need to know the sequence of unix commands and ucsc utilities > to run. > > Does anyone know how I can convert the chain/net files into a browser > track (like the pairwise comparisons for human vs mouse, human vs chimp, > etc). I tried using chainToAxt, then axtToBed, but my genomes are in > 2bit format, not in per chr nib files. > > As a result chainToAxt complains: > > $ chainToAxt -bed chr_random.chain cdqaa0.2bit ../cdqaa1/cdqaa1.2bit stdout > Can't open ../cdqaa1/cdqaa1.2bit/chr_random.nib to read: Not a directory > > Do I need to make nib files of the chromosomes ... which is acceptable > as well. > > Thanks for all the help. > > Vince > > Maximilian Haeussler wrote: >> Hi Vince, >> >> I'm having exactly the same problem and started a page on the >> genomewiki a week ago. >> http://genomewiki.cse.ucsc.edu/index.php/Whole_genome_alignment_howto >> >> This won't really help you but as we're exactly in the same situation >> perhaps we can share what worked. >> I've already run into problems at the first step (blastz) because my >> job is running since a week (I don't have a cluster, but really >> shouldn't need one for ~150 MB) as there are a several thousand >> scaffolds. I've asked Hiram on this and he replied: >> -- >> We break up both the query and the >> target sequence into about 10 million base chunks each, >> with 10,000 overlap on the target pieces, then lift the results >> back to chrom pieces. It is even more tricky for these scaffold >> based organisms. When you have a large query scaffold, >> and a tiny target scaffold, the run-time ironically increases >> to days per job. You can kinda cheat by creating a chrUn >> for the target, but this makes chains that span multiple >> scaffolds which is not correct. >> -- >> >> I've started with a script as simple as this: >> ------ >> basedir=/heap/ci/genome-jgi2/indiv >> compdir=/heap/cs/cs2/reftigs >> BLASTZPARAMS="H=2000 Y=3400 L=6000 K=2200" >> >> for i in $basedir/*; do >> blastz $i /heap/cs/cs2/cioSav2.fa $BLASTZPARAMS >> ci2-cs2.lav >> done >> ------ >> >> If you know a better alternative (hiram pointed out that pooling >> scaffolds is not a much better idea either and if I blastz each >> scaffold onto each other, I have to do 35 000 000 blastz invocations >> which is probably not a lot faster). Anyways, I appreciate any >> discussions/hints/questions... >> >> max >> On 08/06/07, Brooke Rhead wrote: >>> Hi Vince, >>> >>> Thanks for looking through the wiki first! As you can see, the scripts >>> for making nets and chains were definitely developed with our specific >>> environment in mind, but one of our developers has this advice for you: >>> >>> --- >>> If he can modify the hardcoded paths in HgAutomate.pm and >>> doSameSpeciesLiftOver.pl to local equivalents, then he should be able >>> to run doSameSpeciesLiftOver.pl -debug locally to see what kind of >>> scripts it dumps out. >>> >>> 'doSameSpeciesLiftOver.pl -continue net' might work if he can provide >>> his own chained alignments. >>> --- >>> >>> I hope this helps. Please let us know if you have further questions. >>> >>> -- >>> Brooke Rhead >>> UCSC Genome Bioinformatics Group >>> >>> >>> >>> Vince Forgetta wrote: >>>> Hi Guys and Gals, >>>> >>>> >>>> I am attempting to generate chain, net and liftOver files for my >>> bacterial >>>> genome builds. What would be the most straightforward way to >>> accomplish >>>> this? I read through the wiki and tried to run the two scripts, >>>> makeLoChain-align.csh or doSameSpeciesLiftOver.pl, but ran into >>> problems >>>> with paths (no /cluster) and cluster queuing. Is there a way to >>> bypass the >>>> alignment step and feed in an alignment file later in the process? >>>> >>>> Thank for the help. >>>> >>>> Vince >>>> >>>> P.S. If necessary, I wouldn't mind writing some code to help out in >>> the >>>> "bypassing". >>>> _______________________________________________ >>>> 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 davide.cittaro at ifom-ieo-campus.it Fri Jun 8 13:51:04 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Fri, 8 Jun 2007 22:51:04 +0200 Subject: [Genome-mirror] poor man's cluster In-Reply-To: <76f031ae0706080533w398a5fd4t606e4a593e834377@mail.gmail.com> References: <76f031ae0706080533w398a5fd4t606e4a593e834377@mail.gmail.com> Message-ID: Hi there! On Jun 8, 2007, at 2:33 PM, Maximilian Haeussler wrote: > Two years ago I was using windows xp running colinux (debian) with > the ucsc source tree. It was working well and very fast (colinux: > native speed, vmware was a quite slower). (to Davide: perhaps better > than on Freebsd ;-) Gee... I don't think so :-) FreeBSD (especially recent 6.x version) has a great memory management algorithm. FreeBSD problem is that is not that user friendly and (maybe too) highly POSIX compliant . > I don't have money for my own cluster, I don't really need one anyways > :-), but there are so many powerful windows machines on this campus > used by secretaries and doing nothing really useful: I wonder if > anyone of you has ever tried a parasol (or e.g. condor)-based cluster > with windows machines and an emulated linux on them? Hey, have you tried to compile it with cygwin? As far as I know you don't need a "real" cluster because every process seems to be not parallel (unless you want a mysql cluster for data storage). If you have enough memory on those machines you may try to load a genome on each one. Nevertheless you need a mysql server, but hg people can give you a better answer :-) d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare 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 Mon Jun 11 09:15:31 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Mon, 11 Jun 2007 09:15:31 -0700 Subject: [Genome-mirror] poor man's cluster In-Reply-To: References: <76f031ae0706080533w398a5fd4t606e4a593e834377@mail.gmail.com> Message-ID: <466D7523.4010609@soe.ucsc.edu> Good Morning Max, Davide: There is a Microsoft HPC solution to use on your Windows systems: http://www.microsoft.com/windowsserver2003/ccs/default.mspx I think it is only about $400 license per node. The trick to informatics pipelines on clusters is the data situation. Each individual job usually requires quite a bit of data compared to the actual compute load. If you can get a copy of the genome in question to reside in the same place on each node, then you have a chance of getting it to work. I see no fundamental reason why the Kent parasol program wouldn't work compiled with cygwin on a windows box. It would be an interesting experiment, but not something we'll be experimenting with here. --Hiram Davide Cittaro wrote: > Hi there! > > On Jun 8, 2007, at 2:33 PM, Maximilian Haeussler wrote: > >> Two years ago I was using windows xp running colinux (debian) with >> the ucsc source tree. It was working well and very fast (colinux: >> native speed, vmware was a quite slower). (to Davide: perhaps better >> than on Freebsd ;-) > > Gee... I don't think so :-) FreeBSD (especially recent 6.x version) > has a great memory management algorithm. FreeBSD problem is that is > not that user friendly and (maybe too) highly POSIX compliant . > >> I don't have money for my own cluster, I don't really need one anyways >> :-), but there are so many powerful windows machines on this campus >> used by secretaries and doing nothing really useful: I wonder if >> anyone of you has ever tried a parasol (or e.g. condor)-based cluster >> with windows machines and an emulated linux on them? > > Hey, have you tried to compile it with cygwin? As far as I know you > don't need a "real" cluster because every process seems to be not > parallel (unless you want a mysql cluster for data storage). If you > have enough memory on those machines you may try to load a genome on > each one. Nevertheless you need a mysql server, but hg people can > give you a better answer :-) > > d > > > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > 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 hiram at soe.ucsc.edu Mon Jun 11 09:27:05 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Mon, 11 Jun 2007 09:27:05 -0700 Subject: [Genome-mirror] Make my own Chain, Net and LiftOver -- Path of least resistance In-Reply-To: <4669BDE4.1020209@gmail.com> References: <4668990C.1010703@soe.ucsc.edu> <76f031ae0706080517j56f31813k7e89ad20b4a8107a@mail.gmail.com> <4669BDE4.1020209@gmail.com> Message-ID: <466D77D9.3000809@soe.ucsc.edu> Good Morning Max, Vince: You load your chains and nets into tracks with the loaders: hgLoadChain and hgLoadNet But you knew that, or did you want to make a conservation track ? That's a lot more work after you have your chains and nets. Take a look at the ce4.txt described sequence: ## 5-Way multiple alignment # ANNOTATE MULTIZ5WAY MAF AND LOAD TABLES # MULTIZ5WAY MAF FRAMES # CREATE CONSERVATION WIGGLE WITH PHASTCONS - 5-WAY You will need to fetch the multiz program from Penn State: http://www.bx.psu.edu/miller_lab/ And phastCons from Cornell: http://compgen.bscb.cornell.edu/~acs/software.html --Hiram Vincenzo Forgetta wrote: > Hi all, > > Got my liftover files! Turns out it was easier to follow the > instructions in jksrc/kent/src/hg/doc/liftOver.txt. My genomes are ~4Mb > so I don't need any of the automation stuff included in the perl scripts > ... I just need to know the sequence of unix commands and ucsc utilities > to run. > > Does anyone know how I can convert the chain/net files into a browser > track (like the pairwise comparisons for human vs mouse, human vs chimp, > etc). I tried using chainToAxt, then axtToBed, but my genomes are in > 2bit format, not in per chr nib files. > > As a result chainToAxt complains: > > $ chainToAxt -bed chr_random.chain cdqaa0.2bit ../cdqaa1/cdqaa1.2bit stdout > Can't open ../cdqaa1/cdqaa1.2bit/chr_random.nib to read: Not a directory > > Do I need to make nib files of the chromosomes ... which is acceptable > as well. > > Thanks for all the help. > > Vince > > Maximilian Haeussler wrote: >> Hi Vince, >> >> I'm having exactly the same problem and started a page on the >> genomewiki a week ago. >> http://genomewiki.cse.ucsc.edu/index.php/Whole_genome_alignment_howto >> >> This won't really help you but as we're exactly in the same situation >> perhaps we can share what worked. >> I've already run into problems at the first step (blastz) because my >> job is running since a week (I don't have a cluster, but really >> shouldn't need one for ~150 MB) as there are a several thousand >> scaffolds. I've asked Hiram on this and he replied: >> -- >> We break up both the query and the >> target sequence into about 10 million base chunks each, >> with 10,000 overlap on the target pieces, then lift the results >> back to chrom pieces. It is even more tricky for these scaffold >> based organisms. When you have a large query scaffold, >> and a tiny target scaffold, the run-time ironically increases >> to days per job. You can kinda cheat by creating a chrUn >> for the target, but this makes chains that span multiple >> scaffolds which is not correct. >> -- >> >> I've started with a script as simple as this: >> ------ >> basedir=/heap/ci/genome-jgi2/indiv >> compdir=/heap/cs/cs2/reftigs >> BLASTZPARAMS="H=2000 Y=3400 L=6000 K=2200" >> >> for i in $basedir/*; do >> blastz $i /heap/cs/cs2/cioSav2.fa $BLASTZPARAMS >> ci2-cs2.lav >> done >> ------ >> >> If you know a better alternative (hiram pointed out that pooling >> scaffolds is not a much better idea either and if I blastz each >> scaffold onto each other, I have to do 35 000 000 blastz invocations >> which is probably not a lot faster). Anyways, I appreciate any >> discussions/hints/questions... >> >> max >> On 08/06/07, Brooke Rhead wrote: >>> Hi Vince, >>> >>> Thanks for looking through the wiki first! As you can see, the scripts >>> for making nets and chains were definitely developed with our specific >>> environment in mind, but one of our developers has this advice for you: >>> >>> --- >>> If he can modify the hardcoded paths in HgAutomate.pm and >>> doSameSpeciesLiftOver.pl to local equivalents, then he should be able >>> to run doSameSpeciesLiftOver.pl -debug locally to see what kind of >>> scripts it dumps out. >>> >>> 'doSameSpeciesLiftOver.pl -continue net' might work if he can provide >>> his own chained alignments. >>> --- >>> >>> I hope this helps. Please let us know if you have further questions. >>> >>> -- >>> Brooke Rhead >>> UCSC Genome Bioinformatics Group >>> >>> >>> >>> Vince Forgetta wrote: >>>> Hi Guys and Gals, >>>> >>>> >>>> I am attempting to generate chain, net and liftOver files for my >>> bacterial >>>> genome builds. What would be the most straightforward way to >>> accomplish >>>> this? I read through the wiki and tried to run the two scripts, >>>> makeLoChain-align.csh or doSameSpeciesLiftOver.pl, but ran into >>> problems >>>> with paths (no /cluster) and cluster queuing. Is there a way to >>> bypass the >>>> alignment step and feed in an alignment file later in the process? >>>> >>>> Thank for the help. >>>> >>>> Vince >>>> >>>> P.S. If necessary, I wouldn't mind writing some code to help out in >>> the >>>> "bypassing". From hiram at soe.ucsc.edu Mon Jun 11 12:18:59 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Mon, 11 Jun 2007 12:18:59 -0700 Subject: [Genome-mirror] [Genome] Problems with mirror site at MCW: error message "The table 'userDb' is full" In-Reply-To: <4669DF01.70203@cse.ucsc.edu> References: <6FF91AE4F1DC7743A6466E334EB865AE1C1EB9D3@VERITY.roswellpark.org> <4669DF01.70203@cse.ucsc.edu> Message-ID: <466DA023.8050407@soe.ucsc.edu> Good Afternoon Liang and other genome-mirror folks: Please note the cleaner script for the userDb and sessionDb tables in hgcentral: http://genomewiki.ucsc.edu/index.php/Image:CleanHgCentral_pl.txt Also added to the source tree this morning in src/product/cleanHgCentral.pl.txt --Hiram From hiram at soe.ucsc.edu Mon Jun 11 15:00:58 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Mon, 11 Jun 2007 15:00:58 -0700 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> Message-ID: <466DC61A.6020305@soe.ucsc.edu> Good Afternoon Davide: Is it possible to describe the situation in which you are getting this error ? You say this only happens on one type of CPU architecture and not others ? It looks like the track you see failing is a custom track. The groupName which seems to make it go bad is an empty string: "" Which should have come from the cart variable .group What does your cart look like for all the *.group variables ? Any of them appear to have no value ? --Hiram Davide Cittaro wrote: > Hi again, > > On Jun 8, 2007, at 1:11 AM, Hiram Clawson wrote: >> >> Put in a debug printout of all the tracks as they are read in >> groupTracks() after they are set up: >> struct grp* grps = hLoadGrps(); >> during their first processing: >> for (grp = grps; grp != NULL; grp = grp->next) >> >> The zero should show up there ? The list is being >> added to with: >> AllocVar(group); >> slAddHead(&list, group); >> >> and filled in: >> hashAdd(hash, grp->name, group); >> group->name = cloneString(grp->name); >> group->label = cloneString(grp->label); > > Actually, the first element of pTrackList makes all this crash (and > other elements too if I allow a "jump", but let's stay on the first). > Before line 12836 > > 12836 if (hashFindVal(hash, groupName)!=NULL) > 12837 { > 12838 track->groupName = cloneString(groupName); > 12839 track->group = hashFindVal(hash, groupName); > 12840 } > > I have this first track: > > p *track > $22 = {next = 0x9ab7600, mapName = 0x9a81310 "ct_CC", visibility = > tvDense, limitedVis = tvHide, > limitedVisSet = 0, longLabel = 0x98b6ce0 "CC_RARE", shortLabel = > 0x98b6cd0 "CC", mapsSelf = 0 '\0', > drawName = 0 '\0', colorShades = 0x0, color = {r = 0 '\0', g = 0 '\0', > b = 0 '\0'}, ixColor = 0 '\0', > altColorShades = 0x0, altColor = {r = 127 '\177', g = 127 '\177', b = > 127 '\177'}, ixAltColor = 0 '\0', > loadItems = 0x8061c60 , items = 0x0, itemName = > 0x804b90c , > mapItemName = 0x8061de0 , totalHeight = 0x804ace0 > , > height = 0, lineHeight = 10, heightPer = 9, itemHeight = 0x804a8a4 > , > drawItems = 0x804e7b8 , drawItemAt = 0x804cf50 > , > itemStart = 0x804edfc , itemEnd = 0x804ee08 > , > freeItems = 0x804b958 , itemColor = 0, > itemNameColor = 0x804ccc4 , itemLabelColor = > 0, mapItem = 0, hasUi = 1, > extraUiData = 0x9a81330, trackFilter = 0, customPt = 0x942e580, > customInt = 0, subType = 0, > minRange = 0, maxRange = 0, scaleRange = 0, bedSize = 12, otherDb = > 0x0, private = 0, priority = 10, > defaultPriority = 10, groupName = 0x98b6d30 "user", group = 0x9aba0e0, > defaultGroupName = 0x0, > canPack = 1, ss = 0x0, tdb = 0x942e600, expScale = 0, expTable = 0x0, > exonArrows = 1, > exonArrowsAlways = 0, nextItemButtonable = 1, labelNextItemButtonable > = 0, itemAttrTbl = 0x0, > labelColor = 0 '\0', drawLeftLabels = 0, subtracks = 0x0, > nextPrevItem = 0x804b9d0 , > labelNextPrevItem = 0x804bd74 , > loadTime = 0, drawTime = 0} > > and its group > > p *track->group > $24 = {next = 0x9aba100, name = 0x9a81380 "user", label = 0x9a81390 > "Custom Tracks", priority = 1, > defaultPriority = 1, trackList = 0x0} > > This means to me that the track, its group and whatever else is loaded > correctly and works fine. After the "if" block, I have > > p *track > $25 = {next = 0x9ab7600, mapName = 0x9a81310 "ct_CC", visibility = > tvDense, limitedVis = tvHide, > limitedVisSet = 0, longLabel = 0x98b6ce0 "CC_RARE", shortLabel = > 0x98b6cd0 "CC", mapsSelf = 0 '\0', > drawName = 0 '\0', colorShades = 0x0, color = {r = 0 '\0', g = 0 '\0', > b = 0 '\0'}, ixColor = 0 '\0', > altColorShades = 0x0, altColor = {r = 127 '\177', g = 127 '\177', b = > 127 '\177'}, ixAltColor = 0 '\0', > loadItems = 0x8061c60 , items = 0x0, itemName = > 0x804b90c , > mapItemName = 0x8061de0 , totalHeight = 0x804ace0 > , > height = 0, lineHeight = 10, heightPer = 9, itemHeight = 0x804a8a4 > , > drawItems = 0x804e7b8 , drawItemAt = 0x804cf50 > , > itemStart = 0x804edfc , itemEnd = 0x804ee08 > , > freeItems = 0x804b958 , itemColor = 0, > itemNameColor = 0x804ccc4 , itemLabelColor = > 0, mapItem = 0, hasUi = 1, > extraUiData = 0x9a81330, trackFilter = 0, customPt = 0x942e580, > customInt = 0, subType = 0, > minRange = 0, maxRange = 0, scaleRange = 0, bedSize = 12, otherDb = > 0x0, private = 0, priority = 10, > defaultPriority = 10, groupName = 0x8f847b0 "", group = 0x0, > defaultGroupName = 0x0, canPack = 1, > ss = 0x0, tdb = 0x942e600, expScale = 0, expTable = 0x0, exonArrows = > 1, exonArrowsAlways = 0, > nextItemButtonable = 1, labelNextItemButtonable = 0, itemAttrTbl = > 0x0, labelColor = 0 '\0', > drawLeftLabels = 0, subtracks = 0x0, nextPrevItem = 0x804b9d0 > , > labelNextPrevItem = 0x804bd74 , > loadTime = 0, drawTime = 0} > > and, of course > > p *track->group > Error accessing memory address 0x0: Bad address. > > HTH > > d From davide.cittaro at ifom-ieo-campus.it Tue Jun 12 02:37:43 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Tue, 12 Jun 2007 11:37:43 +0200 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: <466DC61A.6020305@soe.ucsc.edu> References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> <466DC61A.6020305@soe.ucsc.edu> Message-ID: Hi again and welcome back :-) On Jun 12, 2007, at 12:00 AM, Hiram Clawson wrote: > Good Afternoon Davide: > > Is it possible to describe the situation in which you are getting > this error ? with a browser: main page->genomes->configure tracks and display->enable track re- ordering this leads to a internal server error. Using Firefox extensions I'm able to transform POST to GET, so that I can catch every argument passed before the crash. I went command line and launched hgTracks with all arguments given before and I have a segmentation fault and a core dump. > You say this only happens on one type of CPU architecture and not > others ? Mmm, actually it is an assumption, since I've tried to compile a little code that accesses NULL pointers on several machines, I haven't tried hgTracks on all those. On linux I assume it works since your main site does! > It looks like the track you see failing is a custom track. The > groupName > which seems to make it go bad is an empty string: "" Mmm, actually every user here has the same problem... > Which should have come from the cart variable .group > What does your cart look like for all the *.group variables ? Any > of them > appear to have no value ? Sorry, I didn't catch this... d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare 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 Tue Jun 12 10:19:32 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Tue, 12 Jun 2007 10:19:32 -0700 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> <466DC61A.6020305@soe.ucsc.edu> Message-ID: <466ED5A4.6000604@soe.ucsc.edu> Good Morning Davide: Something is fishy with your cart variables. A NULL value in this group pointer makes our binaries crash too on Linux. NULL pointers are generally bad on just about any type of architecture. Did you find any architecture in your experiments that would not choke on NULL pointer references ? Take a look at your hgsid number in either your URL, or embedded as a hidden variable in your html output. Use this id (e.g. 1234567) number in the following dump of your session contents: $ hgsql -N -e "select contents from sessionDb where id=1234567;" hgcentral \ | tr '[\&]' '[\n]' | grep group | sed -e "s/.*=//" | sort | uniq -c | sort -n I get approximately this count of tracks in each group: 1 x 2 regulation 2 rna 4 encodeVariation 12 genes 13 encodeCompGeno 15 encodeChrom 17 compGeno 29 varRep 45 encodeTxLevels 71 encodeGenes 74 encodeChip Your exact numbers will vary. What you should NOT see is some kind of garbage name, or a blank name. Verify your central.domain and central.cookie settings in your hg.conf are correct for your location. --Hiram Davide Cittaro wrote: > Hi again and welcome back :-) > On Jun 12, 2007, at 12:00 AM, Hiram Clawson wrote: > >> Good Afternoon Davide: >> >> Is it possible to describe the situation in which you are getting this >> error ? > > with a browser: > main page->genomes->configure tracks and display->enable track re-ordering > > this leads to a internal server error. Using Firefox extensions I'm able > to transform POST to GET, so that I can catch every argument passed > before the crash. I went command line and launched hgTracks with all > arguments given before and I have a segmentation fault and a core dump. > >> You say this only happens on one type of CPU architecture and not others ? > > Mmm, actually it is an assumption, since I've tried to compile a little > code that accesses NULL pointers on several machines, I haven't tried > hgTracks on all those. On linux I assume it works since your main site does! > >> It looks like the track you see failing is a custom track. The groupName >> which seems to make it go bad is an empty string: "" > > Mmm, actually every user here has the same problem... > >> Which should have come from the cart variable .group >> What does your cart look like for all the *.group variables ? Any of them >> appear to have no value ? > > Sorry, I didn't catch this... > > d From davide.cittaro at ifom-ieo-campus.it Tue Jun 12 12:50:13 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Tue, 12 Jun 2007 21:50:13 +0200 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: <466ED5A4.6000604@soe.ucsc.edu> References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> <466DC61A.6020305@soe.ucsc.edu> <466ED5A4.6000604@soe.ucsc.edu> Message-ID: Good afternoon Hiram, On Jun 12, 2007, at 7:19 PM, Hiram Clawson wrote: > Good Morning Davide: > > > Your exact numbers will vary. What you should NOT see is some kind > of garbage > name, or a blank name. I have all regular names > Verify your central.domain and central.cookie settings > in your hg.conf are correct for your location. central.cookie? What's this? It was not mentioned on mirror procedures (actually not when I mirrored for the first time)... What I'm supposed to set there? According to wiki should be something like this: hguid.genome (my web is genome.ifom-ieo-campus.it)? Where I can find then a complete description of all possible values in hg.conf? Tomorrow I'll try to set this central.cookie, I'll tell you what happens next. 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)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From davide.cittaro at ifom-ieo-campus.it Wed Jun 13 00:57:48 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 13 Jun 2007 09:57:48 +0200 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> <466DC61A.6020305@soe.ucsc.edu> <466ED5A4.6000604@soe.ucsc.edu> Message-ID: On Jun 12, 2007, at 9:50 PM, Davide Cittaro wrote: > Tomorrow I'll try to set this central.cookie, I'll tell you what > happens next. > I'm speechless: I've set central.cookie=hguid.genome and everything works. Thanks for the advice and the help so far. d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From davide.cittaro at ifom-ieo-campus.it Wed Jun 13 02:15:44 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Wed, 13 Jun 2007 11:15:44 +0200 Subject: [Genome-mirror] hgTracks bug? In-Reply-To: References: <46674517.80401@soe.ucsc.edu> <466890B3.5020905@soe.ucsc.edu> <94E6891F-F16C-4B05-B645-A83E6867F574@ifom-ieo-campus.it> <466DC61A.6020305@soe.ucsc.edu> <466ED5A4.6000604@soe.ucsc.edu> Message-ID: <24AEA78C-1933-4865-906D-EE317454E7F1@ifom-ieo-campus.it> On Jun 13, 2007, at 9:57 AM, Davide Cittaro wrote: > On Jun 12, 2007, at 9:50 PM, Davide Cittaro wrote: > >> Tomorrow I'll try to set this central.cookie, I'll tell you what >> happens next. >> > > I'm speechless: I've set central.cookie=hguid.genome and everything > works. > Thanks for the advice and the help so far. > False alarm... it seemed to work but it does not... > d > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303007 > e-mail: davide.cittaro at ifom-ieo-campus.it > */ > > /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From davide.cittaro at ifom-ieo-campus.it Thu Jun 14 08:43:25 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Thu, 14 Jun 2007 17:43:25 +0200 Subject: [Genome-mirror] hgTracks security issue? Message-ID: <4133E275-9EC4-41B3-A7C0-8A13EDA1B900@ifom-ieo-campus.it> Hi genome people, while I was playing with my hgTracks errors, I've noticed a possible security issue in hgTracks. Let's say I'm working and I have the hguid cookie set to x and another person has it set to y, I can edit my browser cookie to y so that I can browse other person settings, custom tracks and even delete/modify them. Actually I can't say how severe is this, also I haven't check how this behaves with hgsessions, btw it is not nice that someone can see my work. Cheers d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From galt at soe.ucsc.edu Thu Jun 14 16:17:01 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Thu, 14 Jun 2007 16:17:01 -0700 (PDT) Subject: [Genome-mirror] hgTracks security issue? Message-ID: We're well aware of this issue and have plans to address it in the future. One workaround is to create your own mirror site and control the security on it through whatever mechanism you like - perhaps https and basic authentication via apache configuration. ---------- Forwarded message ---------- Date: Thu, 14 Jun 2007 17:43:25 +0200 From: Davide Cittaro To: genome-mirror at cse.ucsc.edu Subject: [Genome-mirror] hgTracks security issue? Hi genome people, while I was playing with my hgTracks errors, I've noticed a possible security issue in hgTracks. Let's say I'm working and I have the hguid cookie set to x and another person has it set to y, I can edit my browser cookie to y so that I can browse other person settings, custom tracks and even delete/modify them. Actually I can't say how severe is this, also I haven't check how this behaves with hgsessions, btw it is not nice that someone can see my work. Cheers d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare 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 -Galt From rhead at soe.ucsc.edu Fri Jun 15 10:51:46 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Fri, 15 Jun 2007 10:51:46 -0700 Subject: [Genome-mirror] ~24G data to be added to hg17 on Monday Message-ID: <4672D1B2.3070100@soe.ucsc.edu> Hello mirror sites, We plan on adding about 24G of new data to the /gbdb/hg17 directory on Monday. This is to support four new tracks of Affymetrix data, which will be released soon. Please let us know if you have any questions or concerns. -- Brooke Rhead UCSC Genome Bioinformatics Group From reiner.schulz at kcl.ac.uk Mon Jun 18 02:05:01 2007 From: reiner.schulz at kcl.ac.uk (Reiner Schulz) Date: Mon, 18 Jun 2007 10:05:01 +0100 Subject: [Genome-mirror] hgTracks security issue? In-Reply-To: References: Message-ID: <46764ABD.6020701@kcl.ac.uk> just FYI, https works fine for our mirror site. the only limitation: no name-based virtual hosts are supported, i.e., one cannot configure apache to host separate https://a.your.domain.name and https://b.your.domain.name virtual servers, which one can using plain http and which can be useful for running a production and a development version of the browser on the same web server. however, port-based virtual hosts still work w/ https so that one can have, for example, separately configured https://a.your.domain.name:443 and https://a.your.domain.name:886 virtual hosts. r Galt Barber wrote: > We're well aware of this issue and have plans to address > it in the future. One workaround is to create your own > mirror site and control the security on it through whatever > mechanism you like - perhaps https and basic authentication > via apache configuration. > > > ---------- Forwarded message ---------- > Date: Thu, 14 Jun 2007 17:43:25 +0200 > From: Davide Cittaro > To: genome-mirror at cse.ucsc.edu > Subject: [Genome-mirror] hgTracks security issue? > > Hi genome people, > while I was playing with my hgTracks errors, I've noticed a possible > security issue in hgTracks. > Let's say I'm working and I have the hguid cookie set to x and > another person has it set to y, I can edit my browser cookie to y so > that I can browse other person settings, custom tracks and even > delete/modify them. > Actually I can't say how severe is this, also I haven't check how > this behaves with hgsessions, btw it is not nice that someone can see > my work. > > Cheers > > d > > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > 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 > > > > -Galt > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror -- (*)->[]->()->[]->(**)->[]->()->[]->(*)->[]->()->[]->()->[]->()->[]->()->[] (Humboldt University Berlin, Germany)->[]-> ... (University of Maryland, USA)->[]-> ... (King's College London, UK) https://josh.umds.ac.uk/~rschulz From zhai at salk.edu Mon Jun 18 16:19:33 2007 From: zhai at salk.edu (Yufeng Zhai) Date: Mon, 18 Jun 2007 16:19:33 -0700 Subject: [Genome-mirror] How add GFF format tracks to genome browser database. Message-ID: Dear Sir or Madam I have installed genome browser on my computer, and it's no problem for me to add tracks that in psl format to the database. Now I have some problems on adding conservation tracks that in GFF fromat, because I can't find any loader program that can input them to database, My question is how can I add gff formated data into track tables, should I convert them to Bed format by myself? or you have any other straightforward methods? Thank you very much Regards Yufeng From hiram at soe.ucsc.edu Mon Jun 18 16:32:40 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Mon, 18 Jun 2007 16:32:40 -0700 Subject: [Genome-mirror] How add GFF format tracks to genome browser database. In-Reply-To: References: Message-ID: <46771618.5090306@soe.ucsc.edu> Good Afternoon Yufeng: Please note the description of acceptable GFF format custom track files at: http://genome.ucsc.edu/goldenPath/help/customTrack.html#GFF Especially the note about "must be tab separated". If you are trying to cut and paste between windows on your desktop, that cut and paste may not necessarily carry over the tabs properly. Better to leave your GFF data in a file, and "browse ..." to upload the file, or place it on a WEB server and fetch it via a URL. --Hiram Yufeng Zhai wrote: > Dear Sir or Madam > > I have installed genome browser on my computer, and it's no problem > for me to add tracks that in psl format to the database. Now I have > some problems on adding conservation tracks that in GFF fromat, > because I can't find any loader program that can input them to database, > > My question is how can I add gff formated data into track tables, > should I convert them to Bed format by myself? or you have any other > straightforward methods? > > Thank you very much > > Regards > > Yufeng From hiram at soe.ucsc.edu Mon Jun 18 16:35:41 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Mon, 18 Jun 2007 16:35:41 -0700 Subject: [Genome-mirror] How add GFF format tracks to genome browser database. In-Reply-To: <46771618.5090306@soe.ucsc.edu> References: <46771618.5090306@soe.ucsc.edu> Message-ID: <467716CD.7060008@soe.ucsc.edu> For permanent tracks in your local browser, use the "ldHgGene" loader to load gff files. There are a number of peculiar options to the program. Some experimentation may be required. See also the uses of ldHgGene in the numerous example in the make*.txt files in the source tree directory: src/hg/makeDb/doc/*.txt --Hiram Hiram Clawson wrote: > Good Afternoon Yufeng: > > Please note the description of acceptable GFF format custom track files at: > http://genome.ucsc.edu/goldenPath/help/customTrack.html#GFF > > Especially the note about "must be tab separated". If you are trying to > cut and paste between windows on your desktop, that cut and paste > may not necessarily carry over the tabs properly. Better to leave your > GFF data in a file, and "browse ..." to upload the file, or place it > on a WEB server and fetch it via a URL. > > --Hiram > > Yufeng Zhai wrote: >> Dear Sir or Madam >> >> I have installed genome browser on my computer, and it's no problem >> for me to add tracks that in psl format to the database. Now I have >> some problems on adding conservation tracks that in GFF fromat, >> because I can't find any loader program that can input them to database, >> >> My question is how can I add gff formated data into track tables, >> should I convert them to Bed format by myself? or you have any other >> straightforward methods? >> >> Thank you very much >> >> Regards >> >> Yufeng > From aamp at ucsc.edu Mon Jun 18 16:45:04 2007 From: aamp at ucsc.edu (Andy Pohl) Date: Mon, 18 Jun 2007 16:45:04 -0700 Subject: [Genome-mirror] v161 genome browser available Message-ID: <9fa943760706181645v68cace16he0de4d985f22ed2a@mail.gmail.com> Hello, v161 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v161.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 v161 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v161-preview and v161-final to see all the code and data changes in this release. Andy Pohl UCSC CBSE From ann at soe.ucsc.edu Tue Jun 19 13:39:04 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Tue, 19 Jun 2007 13:39:04 -0700 Subject: [Genome-mirror] felCat3 Conservation data on hgnfs1 Message-ID: <46783EE8.10908@cse.ucsc.edu> Hi Mirror Sites, Please be warned that tomorrow we will be placing a large amount of data on the hgnfs1 server. Be prepared to host approximately 8.5 GB of data to support the new felCat3 (cat) Conservation track. /gbdb/felCat3/multiz4way/anno/felCat3.maf ~7.3 GB /gbdb/felCat3/multiz4way/phastCons4way.wib ~1.2 GB Please let us know if you have questions or concerns. Thanks, Ann. From kuhn at soe.ucsc.edu Wed Jun 20 10:38:17 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Wed, 20 Jun 2007 10:38:17 -0700 Subject: [Genome-mirror] dropping some table from hg16 Message-ID: <200706201738.KAA19087@moondance.cse.ucsc.edu> hello mirrors, we are dropping 5.8 Gb of tables from the human assembly database, hg16. these tables were superceded but never removed from our servers. They are: *Mm4* and include chain and net alignments for an archived mouse assembly. we apologize if they have been hogging some of your disk space. thanks, --b0b kuhn ucsc genome bionformatics group From ann at soe.ucsc.edu Wed Jun 20 14:34:23 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Wed, 20 Jun 2007 14:34:23 -0700 Subject: [Genome-mirror] new Conservation track for hg18 Message-ID: <46799D5F.9000807@cse.ucsc.edu> Hi Mirror Folks, Please be warned that as early as tomorrow, we will be placing a large amount of data (about 77 GB) on the hgnfs1 (/gbdb) server. This is to support the new 28-way Conservation track on hg18 (which will actually be released in a few days). Here's a list of the new files: /gbdb/hg18/multiz28way/anno/maf/*.maf /gbdb/hg18/multiz28way/{phastCons28way,phastCons28wayPlacMammal}.wib Please let us know if you have any questions or concerns. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu From jlchang at broad.mit.edu Wed Jun 27 11:47:28 2007 From: jlchang at broad.mit.edu (Jean Chang) Date: Wed, 27 Jun 2007 14:47:28 -0400 Subject: [Genome-mirror] custom track questions Message-ID: <52E54868-6875-40B9-B268-8934CF5E4DA6@broad.mit.edu> Hi, Where would I find information about how uploaded custom tracks are handled on the server side? and ways to have custom tracks persist at our internal mirror? Also, what are the best sources of information about implementing the custom track database? Thanks, Jean From zhai at salk.edu Wed Jun 27 12:03:34 2007 From: zhai at salk.edu (Yufeng Zhai) Date: Wed, 27 Jun 2007 12:03:34 -0700 Subject: [Genome-mirror] How to change the Message-ID: Dear Sir or Madam: I installed a genome browser on my computer and loaded some expression tracks, everything works good, the expression blocks can show different expression values in different grey scales. My question is: How can I change the configurations for those grey color definition? for example, I want to make the color of expression value 2000 lighter than default. Thank you very much Yufeng From rhead at soe.ucsc.edu Wed Jun 27 17:52:09 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Wed, 27 Jun 2007 17:52:09 -0700 Subject: [Genome-mirror] How to change the In-Reply-To: References: Message-ID: <46830639.9030509@soe.ucsc.edu> Hello Yufeng, I spoke to one of our developers familiar with expression tracks. He said that there is one setting that can be changed to affect the color of range of expression data: expScale. (I'm not sure if this is what your question is referring to, however.) The expScale setting is described in our wiki, here: http://genomewiki.cse.ucsc.edu/index.php/Microarray_track Other than this setting, the only other way to change the intensity of expression data would be to transform all of your data so that they show up as lighter or darker in the Browser. OR, perhaps you are referring to the grey color that is displayed when data is missing. For missing data, we use a default value of -10,000, which shows up as a grey color in the Browser that is not easily mistaken for the red, green, or black that is displayed for actual data. There are no settings to change this grey color. Also be aware that any number other than -10,000 will register as real data, not as missing data. -- Brooke Rhead UCSC Genome Bioinformatics Group Yufeng Zhai wrote: > Dear Sir or Madam: > > I installed a genome browser on my computer and loaded some > expression tracks, everything works good, the expression blocks can > show different expression values in different grey scales. > > My question is: How can I change the configurations for those grey > color definition? for example, I want to make the color of expression > value 2000 lighter than default. > > Thank you very much > > Yufeng > > _______________________________________________ > 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 Thu Jun 28 11:53:19 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Thu, 28 Jun 2007 11:53:19 -0700 Subject: [Genome-mirror] custom track questions In-Reply-To: <52E54868-6875-40B9-B268-8934CF5E4DA6@broad.mit.edu> References: <52E54868-6875-40B9-B268-8934CF5E4DA6@broad.mit.edu> Message-ID: <4684039F.8070701@soe.ucsc.edu> Hello Jean, There is a good page about the custom track database on our wiki, here: http://genomewiki.cse.ucsc.edu/index.php/Using_custom_track_database The same information is also available in the kent source tree at /src/product/README.customTracks.dataBase. I hope this information helps. -- Brooke Rhead UCSC Genome Bioinformatics Group Jean Chang wrote: > Hi, > > Where would I find information about how uploaded custom tracks are > handled on the server side? and ways to have custom tracks persist at > our internal mirror? > > Also, what are the best sources of information about implementing the > custom track database? > > Thanks, > > Jean > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From heather at soe.ucsc.edu Fri Jun 29 11:50:06 2007 From: heather at soe.ucsc.edu (Heather Trumbower) Date: Fri, 29 Jun 2007 18:50:06 -0000 Subject: [Genome-mirror] mm7 and canFam2 In-Reply-To: <4BDB66B394E7784F85ACA43EE36EED2911C40488@NIHCESMLBX.nih.gov> References: <4BDB66B394E7784F85ACA43EE36EED2911C40488@NIHCESMLBX.nih.gov> Message-ID: Thanks for the reminder, I'll get that out there. I'll send you a copy in a few minutes, too. Heather Trumbower UCSC Genome Bioinformatics Group On Thu, 29 Dec 2005, Hoover, David (NIH/CIT) [E] wrote: > Hi, > > Are mm7 and canFam2 available for mirroring? I see that the gbdb and > goldenPath files are available, but the hgcentral database > (http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql) doesn't have > anything for these two yet. > > David Hoover > > Dr. David Hoover, Computational Biologist > Helix Systems Staff, DCSS, CIT, NIH > Bldg. 12B, Rm. 2N207, Bethesda, MD 20892 > Ph: 301-435-2986 Email: hooverdm at mail.nih.gov > From heather at soe.ucsc.edu Fri Jun 29 11:50:13 2007 From: heather at soe.ucsc.edu (Heather Trumbower) Date: Fri, 29 Jun 2007 18:50:13 -0000 Subject: [Genome-mirror] mm7 and canFam2 In-Reply-To: <4BDB66B394E7784F85ACA43EE36EED2911C40488@NIHCESMLBX.nih.gov> References: <4BDB66B394E7784F85ACA43EE36EED2911C40488@NIHCESMLBX.nih.gov> Message-ID: David: The updated hgcentral.sql is attached. It includes mm7 and canFam2. Heather Trumbower UCSC Genome Bioinformatics Group On Thu, 29 Dec 2005, Hoover, David (NIH/CIT) [E] wrote: > Hi, > > Are mm7 and canFam2 available for mirroring? I see that the gbdb and > goldenPath files are available, but the hgcentral database > (http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql) doesn't have > anything for these two yet. > > David Hoover > > Dr. David Hoover, Computational Biologist > Helix Systems Staff, DCSS, CIT, NIH > Bldg. 12B, Rm. 2N207, Bethesda, MD 20892 > Ph: 301-435-2986 Email: hooverdm at mail.nih.gov > -------------- next part -------------- -- MySQL dump 9.11 -- -- Host: localhost Database: hgcentral -- ------------------------------------------------------ -- Server version 4.0.25 -- -- Table structure for table `sessionDb` -- CREATE TABLE sessionDb ( id int(10) unsigned NOT NULL auto_increment, contents longblob NOT NULL, reserved tinyint(4) NOT NULL default '0', firstUse datetime NOT NULL default '0000-00-00 00:00:00', lastUse datetime NOT NULL default '0000-00-00 00:00:00', useCount int(11) NOT NULL default '0', PRIMARY KEY (id) ) TYPE=MyISAM; -- -- Table structure for table `userDb` -- CREATE TABLE userDb ( id int(10) unsigned NOT NULL auto_increment, contents longblob NOT NULL, reserved tinyint(4) NOT NULL default '0', firstUse datetime NOT NULL default '0000-00-00 00:00:00', lastUse datetime NOT NULL default '0000-00-00 00:00:00', useCount int(11) NOT NULL default '0', PRIMARY KEY (id) ) TYPE=MyISAM PACK_KEYS=1; -- MySQL dump 9.11 -- -- Host: localhost Database: hgcentral -- ------------------------------------------------------ -- Server version 4.0.25 -- -- Table structure for table `defaultDb` -- CREATE TABLE defaultDb ( genome varchar(255) NOT NULL default '', name varchar(255) NOT NULL default '', PRIMARY KEY (genome) ) TYPE=MyISAM; -- -- Dumping data for table `defaultDb` -- INSERT INTO defaultDb (genome, name) VALUES ('Human','hg17'); INSERT INTO defaultDb (genome, name) VALUES ('Mouse','mm7'); INSERT INTO defaultDb (genome, name) VALUES ('Rat','rn3'); INSERT INTO defaultDb (genome, name) VALUES ('Zoo','zooHuman3'); INSERT INTO defaultDb (genome, name) VALUES ('SARS','sc1'); INSERT INTO defaultDb (genome, name) VALUES ('C. elegans','ce2'); INSERT INTO defaultDb (genome, name) VALUES ('C. briggsae','cb1'); INSERT INTO defaultDb (genome, name) VALUES ('Fugu','fr1'); INSERT INTO defaultDb (genome, name) VALUES ('D. melanogaster','dm2'); INSERT INTO defaultDb (genome, name) VALUES ('D. pseudoobscura','dp3'); INSERT INTO defaultDb (genome, name) VALUES ('S. cerevisiae','sacCer1'); INSERT INTO defaultDb (genome, name) VALUES ('Chimp','panTro1'); INSERT INTO defaultDb (genome, name) VALUES ('Chicken','galGal2'); INSERT INTO defaultDb (genome, name) VALUES ('Dog','canFam2'); INSERT INTO defaultDb (genome, name) VALUES ('C. intestinalis','ci2'); INSERT INTO defaultDb (genome, name) VALUES ('D. yakuba','droYak1'); INSERT INTO defaultDb (genome, name) VALUES ('Zebrafish','danRer2'); INSERT INTO defaultDb (genome, name) VALUES ('A. gambiae','anoGam1'); INSERT INTO defaultDb (genome, name) VALUES ('Tetraodon','tetNig1'); INSERT INTO defaultDb (genome, name) VALUES ('X. tropicalis','xenTro1'); INSERT INTO defaultDb (genome, name) VALUES ('D. mojavensis','droMoj2'); INSERT INTO defaultDb (genome, name) VALUES ('A. mellifera','apiMel2'); INSERT INTO defaultDb (genome, name) VALUES ('D. virilis','droVir2'); INSERT INTO defaultDb (genome, name) VALUES ('D. ananassae','droAna2'); INSERT INTO defaultDb (genome, name) VALUES ('Opossum','monDom1'); INSERT INTO defaultDb (genome, name) VALUES ('Cow','bosTau2'); INSERT INTO defaultDb (genome, name) VALUES ('Rhesus','rheMac1'); INSERT INTO defaultDb (genome, name) VALUES ('D. simulans','droSim1'); INSERT INTO defaultDb (genome, name) VALUES ('D. erecta','droEre1'); INSERT INTO defaultDb (genome, name) VALUES ('D. grimshawi','droGri1'); -- -- Table structure for table `blatServers` -- CREATE TABLE blatServers ( db varchar(32) NOT NULL default '', host varchar(128) NOT NULL default '', port int(11) NOT NULL default '0', isTrans tinyint(4) NOT NULL default '0', canPcr tinyint(4) NOT NULL default '0', KEY db (db) ) TYPE=MyISAM PACK_KEYS=1; -- -- Dumping data for table `blatServers` -- INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('galGal2','blat18',17780,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('sc1','blat11',17780,0,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('sc1','blat11',17781,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('hg15','blat15',17790,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('panTro1','blat7',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('panTro1','blat7',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('anoGam1','blat18',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('mm6','blat15',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('mm6','blat15',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('rn2','blat2',17784,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('rn2','blat2',17785,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ce1','blat18',17788,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ce1','blat18',17789,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('cb1','blat18',17787,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('cb1','blat18',17786,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('rn3','blat11',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('rn3','blat11',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dp3','blat18',17798,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dp3','blat18',17799,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droSim1','blat9',17780,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droSim1','blat9',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('hg15','blat15',17791,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('rheMac1','blat10',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('apiMel2','blat14',17792,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('apiMel2','blat14',17793,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('bosTau1','blat13',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('bosTau1','blat13',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dm2','blat14',17795,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dm2','blat14',17794,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('monDom1','blat14',17787,0,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('monDom1','blat14',17786,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('hg16','blat13',17784,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('hg16','blat13',17785,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('fr1','blat11',17783,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('fr1','blat11',17782,0,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dm1','blat18',17794,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dm1','blat18',17795,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('rheMac1','blat10',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('sacCer1','blat18',17800,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('sacCer1','blat18',17801,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('galGal2','blat18',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ce2','blat18',17790,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ce2','blat18',17791,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('tetNig1','blat18',17782,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dp2','blat18',17797,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ci1','blat18',17792,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ci1','blat18',17793,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('mm5','blat13',17783,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('mm5','blat13',17782,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('hg17','blat12',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('hg17','blat12',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droYak1','blat7',17780,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droYak1','blat7',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('danRer1','blat18',17784,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('danRer1','blat18',17785,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('anoGam1','blat18',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('dp2','blat18',17796,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('canFam1','blat9',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('canFam1','blat9',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('tetNig1','blat18',17783,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('xenTro1','blat13',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('xenTro1','blat13',17780,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droMoj1','blat14',17782,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droMoj1','blat14',17783,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droVir1','blat14',17785,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droVir1','blat14',17784,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droAna1','blat14',17780,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droAna1','blat14',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('apiMel1','blat14',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('apiMel1','blat14',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('danRer2','blat14',17788,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('danRer2','blat14',17789,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ci2','blat10',17780,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('ci2','blat10',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droVir2','blat6',17785,0,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droVir2','blat6',17784,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droMoj2','blat6',17787,0,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droMoj2','blat6',17786,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droEre1','blat16',17787,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droEre1','blat16',17786,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('bosTau2','blat16',17782,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('bosTau2','blat16',17783,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droAna2','blat16',17784,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droAna2','blat16',17785,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droGri1','blat6',17782,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('droGri1','blat6',17783,0,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('mm7','blat16',17778,1,0); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('mm7','blat16',17779,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('canFam2','blat19',17781,0,1); INSERT INTO blatServers (db, host, port, isTrans, canPcr) VALUES ('canFam2','blat19',17780,1,0); -- -- Table structure for table `dbDb` -- CREATE TABLE dbDb ( name varchar(32) NOT NULL default '', description varchar(255) NOT NULL default '', nibPath varchar(255) NOT NULL default '', organism varchar(255) NOT NULL default '', defaultPos varchar(255) NOT NULL default '', active int(1) NOT NULL default '0', orderKey int(11) NOT NULL default '1000000', genome varchar(255) NOT NULL default '', scientificName varchar(255) NOT NULL default '', htmlPath varchar(255) NOT NULL default '', hgNearOk tinyint(4) NOT NULL default '0', hgPbOk tinyint(4) NOT NULL default '0', sourceName varchar(255) NOT NULL default '' ) TYPE=MyISAM; -- -- Dumping data for table `dbDb` -- INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('dm1','Jan. 2003','/gbdb/dm1/nib','D. melanogaster','chr2L:827700-845800',1,52,'D. melanogaster','Drosophila melanogaster','/gbdb/dm1/html/description.html',1,0,'BDGP v. 3'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('sc1','Apr. 2003','/gbdb/sc1/nib','SARS','chr1',1,100,'SARS','SARS coronavirus','/gbdb/sc1/html/description.html',0,0,'GenBank sequence as of 14 Apr 2003'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('rn2','Jan. 2003','/gbdb/rn2/nib','Rat','chr5:186572878-186580717',1,31,'Rat','Rattus norvegicus','/gbdb/rn2/html/description.html',1,0,'Baylor HGSC v. 2.1'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('sacCer1','Oct. 2003','/gbdb/sacCer1/nib','S. cerevisiae','chr13:746300-756100',1,80,'S. cerevisiae','Saccharomyces cerevisiae','/gbdb/sacCer1/html/description.html',1,0,'SGD sequence data as of 1 Oct. 2003'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('dp2','Aug. 2003','/gbdb/dp2/nib','D. pseudoobscura','Contig1006_Contig943:3363975-3378814',1,56,'D. pseudoobscura','Drosophila pseudoobscura','/gbdb/dp2/html/description.html',0,0,'Baylor HGSC Freeze 1'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('hg15','Apr. 2003','/gbdb/hg15/nib','Human','chr7:26828631-26938371',1,12,'Human','Homo sapiens','/gbdb/hg15/html/description.html',1,0,'NCBI Build 33'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('ce1','May 2003','/gbdb/ce1/nib','C. elegans','chrII:14642289-14671631',1,61,'C. elegans','Caenorhabditis elegans','/gbdb/ce1/html/description.html',1,0,'WormBase v. WS100'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('cb1','July 2002','/gbdb/cb1/nib','C. briggsae','chrUn:74980670-74998831',1,70,'C. briggsae','Caenorhabditis briggsae','/gbdb/cb1/html/description.html',0,0,'WormBase v. cb25.agp8'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('hg16','July 2003','/gbdb/hg16/nib','Human','chr4:56214201-56291736',1,11,'Human','Homo sapiens','/gbdb/hg16/html/description.html',1,1,'NCBI Build 34'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('rn3','June 2003','/gbdb/rn3/nib','Rat','chr5:169359914-169392264',1,30,'Rat','Rattus norvegicus','/gbdb/rn3/html/description.html',1,1,'Baylor HGSC v. 3.1'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooHuman3','Human','/gbdb/zoo3/nib/zooHuman3','Human','target1',1,1000,'Zoo','Homo sapiens','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooCat3','Cat','/gbdb/zoo3/nib/zooCat3','Cat','target1',1,1003,'Zoo','Felis catus','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooChicken3','Chicken','/gbdb/zoo3/nib/zooChicken3','Chicken','target1',1,1004,'Zoo','Gallus gallus','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooBaboon3','Baboon','/gbdb/zoo3/nib/zooBaboon3','Baboon','target1',1,1002,'Zoo','Papio hamadryas','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooChimp3','Chimpanzee','/gbdb/zoo3/nib/zooChimp3','Chimpanzee','target1',1,1005,'Zoo','Pan troglodytes','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooCow3','Cow','/gbdb/zoo3/nib/zooCow3','Cow','target1',1,1006,'Zoo','Bos taurus','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooDog3','Dog','/gbdb/zoo3/nib/zooDog3','Dog','target1',1,1007,'Zoo','Canus familiaris','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooFugu3','Fugu','/gbdb/zoo3/nib/zooFugu3','Fugu','target1',1,1008,'Zoo','Takifugu rubripes','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooMouse3','Mouse','/gbdb/zoo3/nib/zooMouse3','Mouse','target1',1,1009,'Zoo','Mus musculus','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooPig3','Pig','/gbdb/zoo3/nib/zooPig3','Pig','target1',1,1010,'Zoo','Sus scrofa','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooRat3','Rat','/gbdb/zoo3/nib/zooRat3','Rat','target1',1,1011,'Zoo','Rattus norvegicus','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooTetra3','Tetra','/gbdb/zoo3/nib/zooTetra3','Tetra','target1',1,1012,'Zoo','Tetraodon nigroviridis','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('zooZebrafish3','Zebrafish','/gbdb/zoo3/nib/zooZebrafish3','Zebrafish','target1',1,1013,'Zoo','Danio rerio','/gbdb/zoo3/html/description.html',0,0,''); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('fr1','Aug. 2002','/gbdb/fr1/nib','Fugu','chrUn:148538552-148543911',1,40,'Fugu','Takifugu rubripes','/gbdb/fr1/html/description.html',0,0,'JGI V3.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('panTro1','Nov. 2003','/gbdb/panTro1/nib','Chimp','chr6:115705331-115981791',1,15,'Chimp','Pan troglodytes','/gbdb/panTro1/html/description.html',0,0,'CGSC Build 1 Version 1 Arachne assembly'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('galGal2','Feb. 2004','/gbdb/galGal2/nib','Chicken','chr13:13120186-13124117',1,35,'Chicken','Gallus gallus','/gbdb/galGal2/html/description.html',0,0,'Chicken Genome Sequencing Consortium Feb. 2004 release'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('ce2','Mar. 2004','/gbdb/ce2/nib','C. elegans','chrII:14642289-14671631',1,60,'C. elegans','Caenorhabditis elegans','/gbdb/ce2/html/description.html',1,0,'WormBase v. WS120'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('rheMac1','Jan. 2005','/gbdb/rheMac1','Rhesus','SCAFFOLD125093:168700-200800',1,16,'Rhesus','Macaca Mulatta','/gbdb/rheMac1/html/description.html',0,0,'Baylor v0.1'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('mm6','Mar. 2005','/gbdb/mm6','Mouse','chrX:87947304-87959012',1,24,'Mouse','Mus musculus','/gbdb/mm6/html/description.html',1,1,'NCBI Build 34'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('xenTro1','Oct. 2004','/gbdb/xenTro1','X. tropicalis','scaffold_12:3462738-3490440',1,36,'X. tropicalis','Xenopus tropicalis','/gbdb/xenTro1/html/description.html',0,0,'JGI v3.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('canFam1','July 2004','/gbdb/canFam1/nib','Dog','chr14:10666612-10673232',1,18,'Dog','Canis familiaris','/gbdb/canFam1/html/description.html',0,0,'Broad Institute v. 1.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('ci1','Dec. 2002','/gbdb/ci1/nib','C. intestinalis','Scaffold_490:1-51949',1,45,'C. intestinalis','Ciona intestinalis','/gbdb/ci1/html/description.html',0,0,'JGI v1.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('mm5','May 2004','/gbdb/mm5/nib','Mouse','chr6:28912411-28925620',1,25,'Mouse','Mus musculus','/gbdb/mm5/html/description.html',1,1,'NCBI Build 33'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('hg17','May 2004','/gbdb/hg17/nib','Human','chr7:127471196-127495720',1,10,'Human','Homo sapiens','/gbdb/hg17/html/description.html',1,1,'NCBI Build 35'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droYak1','Apr. 2004','/gbdb/droYak1/nib','D. yakuba','chr2L:827700-845800',1,53,'D. yakuba','Drosophila yakuba','/gbdb/droYak1/html/description.html',0,0,'WUSTL version 1.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('danRer1','Nov. 2003','/gbdb/danRer1/nib','Zebrafish','chr2:16330443-16335196',1,38,'Zebrafish','Danio rerio','/gbdb/danRer1/html/description.html',0,0,'Sanger Centre, Danio rerio Sequencing Project Zv3'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('anoGam1','Feb. 2003','/gbdb/anoGam1/nib','A. gambiae','chr2R:6479796-6482329',1,59,'A. gambiae','Anopheles gambiae','/gbdb/anoGam1/html/description.html',0,0,'IAGEC v.MOZ2'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('tetNig1','Feb. 2004','/gbdb/tetNig1/nib','Tetraodon','chr10:2344000-2351500',1,39,'Tetraodon','Tetraodon nigroviridis','/gbdb/tetNig1/html/description.html',0,0,'Genoscope and Broad Institute, V7'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droMoj1','Aug. 2004','/gbdb/droMoj1','D. mojavensis','contig_2959:30001-44626',1,57,'D. mojavensis','Drosophila mojavensis','/gbdb/droMoj1/html/description.html',0,0,'Agencourt 11 Aug 2004'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('apiMel2','Jan. 2005','/gbdb/apiMel2','A. mellifera','GroupUn:47426601-47431800',1,57,'A. mellifera','Apis mellifera','/gbdb/apiMel2/html/description.html',0,0,'Baylor HGSC Amel_2.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droVir1','July 2004','/gbdb/droVir1','D. virilis','scaffold_6:5128001-5158000',1,57,'D. virilis','Drosophila virilis','/gbdb/droVir1/html/description.html',0,0,'Agencourt 12 July 2004'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droAna1','July 2004','/gbdb/droAna1','D. ananassae','2448876:2700001-2725000',1,57,'D. ananassae','Drosophila ananassae','/gbdb/droAna1/html/description.html',0,0,'TIGR 15 July 2004'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('apiMel1','July 2004','/gbdb/apiMel1','A. mellifera','GroupUn.5651:1001-6000',1,58,'A. mellifera','Apis mellifera','/gbdb/apiMel1/html/description.html',0,0,'Baylor HGSC Amel_1.2'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('danRer2','June 2004','/gbdb/danRer2','Zebrafish','chr2:15,906,734-15,926,406',1,37,'Zebrafish','Danio rerio','/gbdb/danRer2/html/description.html',0,0,'Sanger Centre, Danio rerio Sequencing Project Zv4'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('monDom1','Oct. 2004','/gbdb/monDom1','Opossum','scaffold_18580:4449881-4565227',1,34,'Opossum','Monodelphis domestica','/gbdb/monDom1/html/description.html',0,0,'Broad Inst. Prelim Oct04'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('dm2','Apr. 2004','/gbdb/dm2/nib','D. melanogaster','chr2L:825964-851061',1,51,'D. melanogaster','Drosophila melanogaster','/gbdb/dm2/html/description.html',0,0,'BDGP v. 4 / DHGP v. 3.2'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('bosTau1','Sep. 2004','/gbdb/bosTau1','Cow','SCAFFOLD100016:1-30000',1,19,'Cow','Bos taurus','/gbdb/bosTau1/html/description.html',0,0,'Baylor v1.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('dp3','Nov. 2004','/gbdb/dp3','D. pseudoobscura','chr4_group3:5603001-5614000',1,56,'D. pseudoobscura','Drosophila pseudoobscura','/gbdb/dp3/html/description.html',0,0,'FlyBase Release 1.03'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droSim1','Apr. 2005','/gbdb/droSim1','D. simulans','chr2L:827,150-853,526',1,52,'D. simulans','Drosophila simulans','/gbdb/droSim1/html/description.html',0,0,'WUSTL version 1.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('mm3','Feb. 2003','/gbdb/mm3/nib','Mouse','chr6:121947466-121963394',0,27,'Mouse','Mus musculus','/gbdb/mm3/html/description.html',0,0,'NCBI Build 30'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('ci2','Mar. 2005','/gbdb/ci2/nib','C. intestinalis','chr01p:3,108,502-3,170,702',1,44,'C. intestinalis','Ciona intestinalias','/gbdb/ci2/html/description.html',0,0,'JGI v2.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droVir2','Aug. 2005','/gbdb/droVir2','D. virilis','scaffold_12963:19375824-19416317',1,57,'D. virilis','Drosophila virilis','/gbdb/droVir2/html/description.html',0,0,'Agencourt 1 August 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droMoj2','Aug. 2005','/gbdb/droMoj2','D. mojavensis','scaffold_6500:23838548-23875233',1,57,'D. mojavensis','Drosophila mojavensis','/gbdb/droMoj2/html/description.html',0,0,'Agencourt 1 August 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droEre1','Aug. 2005','/gbdb/droEre1','D. erecta','scaffold_4929:882464-907886',1,53,'D. erecta','Drosophila erecta','/gbdb/droEre1/html/description.html',0,0,'Agencourt 1 Aug 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('bosTau2','Mar. 2005','/gbdb/bosTau2','Cow','SCAFFOLD10671:4650-8779',1,19,'Cow','Bos taurus','/gbdb/bosTau2/html/description.html',0,0,'Baylor Btau_2.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droAna2','Aug. 2005','/gbdb/droAna2','D. ananassae','scaffold_12916:2717000-2741384',1,54,'D. ananassae','Drosophila ananassae','/gbdb/droAna2/html/description.html',0,0,'Agencourt 1 August 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('droGri1','Aug. 2005','/gbdb/droGri1','D. grimshawi','scaffold_24862:854980-869643',1,57,'D. grimshawi','Drosophila grimshawi','/gbdb/droGri1/html/description.html',0,0,'Agencourt 1 Aug 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('mm7','Aug. 2005','/gbdb/mm7','Mouse','chr2:146923205-146928018',1,23,'Mouse','Mus musculus','/gbdb/mm7/html/description.html',1,1,'NCBI Build 35'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('canFam2','May 2005','/gbdb/canFam2','Dog','chr14:11072309-11078928',1,18,'Dog','Canis familiaris','/gbdb/canFam2/html/description.html',0,0,'Broad Institute v. 2.0'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('dasNov1','May. 2005','/gbdb/dasNov1','Armadillo','scaffold_4294:1-90,852',0,32,'Armadillo','Dasypus novemcinctus','/gbdb/dasNov1/html/description.html',0,0,'Broad May 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('loxAfr1','May. 2005','/gbdb/loxAfr1','Elephant','scaffold_197:6,946-230,632',0,33,'Elephant','Loxodonta africana','/gbdb/loxAfr1/html/description.html',0,0,'Broad May 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('monDom2','June 2005','/gbdb/monDom2','Opossum','scaffold_0:1000000-11000000',0,34,'Opossum','Monodelphis domestica','/gbdb/monDom2/html/description.html',0,0,'Broad Inst. V3 Prelim Jun05'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('danRer3','May 2005','/gbdb/danRer3','Zebrafish','chr13:15,409,989-15,425,511',0,37,'Zebrafish','Danio rerio','/gbdb/danRer3/html/description.html',0,0,'Sanger Centre, Danio rerio Sequencing Project Zv5'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('oryCun1','May. 2005','/gbdb/oryCun1','Rabbit','scaffold_203931:16852-20386',0,32,'Rabbit','Oryctolagus cuniculus','/gbdb/oryCun1/html/description.html',0,0,'Broad May 2005'); INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName) VALUES ('echTel1','July. 2005','/gbdb/echTel1','Tenrec','scaffold_287419:9,981-66,345',0,57,'Tenrec','Echinops telfairi','/gbdb/echTel1/html/description.html',0,0,'Broad July 2005'); -- -- Table structure for table `gdbPdb` -- CREATE TABLE gdbPdb ( genomeDb char(32) NOT NULL default '', proteomeDb char(32) NOT NULL default '' ) TYPE=MyISAM; -- -- Dumping data for table `gdbPdb` -- INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('hg17','proteins050415'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('hg15','proteins040115'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('mm6','proteins050415'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('rn2','proteins040315'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('rn3','proteins040315'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('hg16','proteins040315'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('default','proteins040315'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('mm5','proteins040515'); INSERT INTO gdbPdb (genomeDb, proteomeDb) VALUES ('mm7','proteins051015'); -- -- Table structure for table `liftOverChain` -- CREATE TABLE liftOverChain ( fromDb varchar(255) NOT NULL default '', toDb varchar(255) NOT NULL default '', path longblob NOT NULL, minMatch float NOT NULL default '0', minSizeT int(10) unsigned NOT NULL default '0', minSizeQ int(10) unsigned NOT NULL default '0', multiple char(1) NOT NULL default '', minBlocks float NOT NULL default '0', fudgeThick char(1) NOT NULL default '' ) TYPE=MyISAM; -- -- Dumping data for table `liftOverChain` -- INSERT INTO liftOverChain (fromDb, toDb, path, minMatch, minSizeT, minSizeQ, multiple, minBlocks, fudgeThick) VALUES ('hg13','hg15','/gbdb/hg13/liftOver/hg13ToHg15.over.chain',0.95,0,0,'N',1,'N'); INSERT INTO liftOverChain (fromDb, toDb, path, minMatch, minSizeT, minSizeQ, multiple, minBlocks, fudgeThick) VALUES ('hg13','hg16','/gbdb/hg13/liftOver/hg13ToHg16.over.chain',0.95,0,0,'N',1,'N'); INSERT INTO liftOverChain (fromDb, toDb, path, minMatch, minSizeT, minSizeQ, multiple, minBlocks, fudgeThick) VALUES ('hg15','hg16','/gbdb/hg15/liftOver/hg15ToHg16.over.chain',0.95,0,0,'N',1,'N'); INSERT INTO liftOverChain (fromDb, toDb, path, minMatch, minSizeT, minSizeQ, multiple, minBlocks, fudgeThick) VALUES ('hg12','hg15','/gbdb/hg12/liftOver/hg12ToHg15.over.chain',0.95,0,0,'N',1,'N'); INSERT INTO liftOverChain (fromDb, toDb, path, minMatch, minSizeT, minSizeQ, multiple, minBlocks, fudgeThick) VALUES ('hg12','hg16','/gbdb/hg12/liftOver/hg12ToHg16.over.chain',0.95