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From: Andrew S. <ac...@ge...> - 2010-04-28 15:38:48
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Hello,
I am viewing the tracks on the JBrowse demo site at
http://jbrowse.org/ucsc/hg19/ and have a couple of questions. What version
of JBrowse is this using? I have attempted to take the trackData.json files
from the demo site and use them in the version of JBrowse that I checked out
from github. Neither branch (master or lazyfeatures) seems to be working.
Specifically, when I add the "Ensembl Genes" track to the display, nothing
is getting rendered. Also, is there any documentation as to how you were
able to generate all of the trackData.json files? I know there is a set of
perl scripts, but a more detailed tutorial (with example files) would be
very useful.
Thanks,
Andrew Shinohara
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From: Ian H. <ih...@be...> - 2010-04-28 16:01:30
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Andrew, You need to do more than just copy trackData.json, you need to actually generate the track files from data (or copy the entire directory tree, I suppose). There are two tutorials linked from jbrowse.org. For future problem reports it could be useful to know what platform you're on (server & client web browser), and what you have typed at the command line. Ian Andrew Shinohara wrote: > Hello, > I am viewing the tracks on the JBrowse demo site at > http://jbrowse.org/ucsc/hg19/ and have a couple of questions. What > version of JBrowse is this using? I have attempted to take the > trackData.json files from the demo site and use them in the version of > JBrowse that I checked out from github. Neither branch (master or > lazyfeatures) seems to be working. Specifically, when I add the > "Ensembl Genes" track to the display, nothing is getting rendered. > Also, is there any documentation as to how you were able to generate all > of the trackData.json files? I know there is a set of perl scripts, but > a more detailed tutorial (with example files) would be very useful. > > Thanks, > Andrew Shinohara > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Andrew S. <ac...@ge...> - 2010-04-28 16:10:29
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Ian,
Sorry I was not more explicit. I have copied the entire directory tree
from the demo site from data all the way down. I am working on OS X with
Firefox 3.6.3. I have firebug up and I am not getting any 404 errors, so it
looks like all of the Ajax requests are working fine.
-Andrew
On Wed, Apr 28, 2010 at 12:01 PM, Ian Holmes <ih...@be...> wrote:
> Andrew,
>
> You need to do more than just copy trackData.json, you need to actually
> generate the track files from data (or copy the entire directory tree, I
> suppose). There are two tutorials linked from jbrowse.org.
>
>
> For future problem reports it could be useful to know what platform you're
> on (server & client web browser), and what you have typed at the command
> line.
>
> Ian
>
>
> Andrew Shinohara wrote:
>
>> Hello,
>> I am viewing the tracks on the JBrowse demo site at
>> http://jbrowse.org/ucsc/hg19/ and have a couple of questions. What
>> version of JBrowse is this using? I have attempted to take the
>> trackData.json files from the demo site and use them in the version of
>> JBrowse that I checked out from github. Neither branch (master or
>> lazyfeatures) seems to be working. Specifically, when I add the "Ensembl
>> Genes" track to the display, nothing is getting rendered. Also, is there
>> any documentation as to how you were able to generate all of the
>> trackData.json files? I know there is a set of perl scripts, but a more
>> detailed tutorial (with example files) would be very useful.
>>
>> Thanks,
>> Andrew Shinohara
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
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From: Ian H. <ih...@be...> - 2010-04-28 17:19:04
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Thanks Andrew, The demo uses the lazyfeatures branch. I can't immediately see what the problem is; given that you are copying from a working demo, it seems like it might well be an httpd config or permissions issue at your end (or an incomplete copy), but it's hard to be sure. Can you try the tutorial(s)? It might be easier to start from scratch. Best wishes, Ian Andrew Shinohara wrote: > Ian, > Sorry I was not more explicit. I have copied the entire directory > tree from the demo site from data all the way down. I am working on OS > X with Firefox 3.6.3. I have firebug up and I am not getting any 404 > errors, so it looks like all of the Ajax requests are working fine. > > -Andrew > > On Wed, Apr 28, 2010 at 12:01 PM, Ian Holmes <ih...@be... > <mailto:ih...@be...>> wrote: > > Andrew, > > You need to do more than just copy trackData.json, you need to > actually generate the track files from data (or copy the entire > directory tree, I suppose). There are two tutorials linked from > jbrowse.org <http://jbrowse.org>. > > > For future problem reports it could be useful to know what platform > you're on (server & client web browser), and what you have typed at > the command line. > > Ian > > > Andrew Shinohara wrote: > > Hello, > I am viewing the tracks on the JBrowse demo site at > http://jbrowse.org/ucsc/hg19/ and have a couple of questions. > What version of JBrowse is this using? I have attempted to > take the trackData.json files from the demo site and use them in > the version of JBrowse that I checked out from github. Neither > branch (master or lazyfeatures) seems to be working. > Specifically, when I add the "Ensembl Genes" track to the > display, nothing is getting rendered. Also, is there any > documentation as to how you were able to generate all of the > trackData.json files? I know there is a set of perl scripts, > but a more detailed tutorial (with example files) would be very > useful. > > Thanks, > Andrew Shinohara > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Andrew S. <ac...@ge...> - 2010-04-28 18:38:13
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Ian, I have tried out the volvox tutorial and was successful, however; I did not see any tutorial as to how your team arrived at a working demo for Homo Sapiens. Did you use the flatfile-to-json.pl script? Where did you obtain the GFF file used in this script? I tried to run this script on a GFF file from: http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr1_ens_annots.gff But it did not produce the desired output. Any more detail as to how you arrived at this working demo for Homo Sapiens would be very helpful. Thanks, Andrew On Wed, Apr 28, 2010 at 1:18 PM, Ian Holmes <ih...@be...> wrote: > > Thanks Andrew, > > The demo uses the lazyfeatures branch. I can't immediately see what the problem is; given that you are copying from a working demo, it seems like it might well be an httpd config or permissions issue at your end (or an incomplete copy), but it's hard to be sure. > > Can you try the tutorial(s)? It might be easier to start from scratch. > > Best wishes, > Ian > > Andrew Shinohara wrote: >> >> Ian, >> Sorry I was not more explicit. I have copied the entire directory tree from the demo site from data all the way down. I am working on OS X with Firefox 3.6.3. I have firebug up and I am not getting any 404 errors, so it looks like all of the Ajax requests are working fine. >> >> -Andrew >> >> On Wed, Apr 28, 2010 at 12:01 PM, Ian Holmes <ih...@be... <mailto:ih...@be...>> wrote: >> >> Andrew, >> >> You need to do more than just copy trackData.json, you need to >> actually generate the track files from data (or copy the entire >> directory tree, I suppose). There are two tutorials linked from >> jbrowse.org <http://jbrowse.org>. >> >> >> For future problem reports it could be useful to know what platform >> you're on (server & client web browser), and what you have typed at >> the command line. >> >> Ian >> >> >> Andrew Shinohara wrote: >> >> Hello, >> I am viewing the tracks on the JBrowse demo site at >> http://jbrowse.org/ucsc/hg19/ and have a couple of questions. >> What version of JBrowse is this using? I have attempted to >> take the trackData.json files from the demo site and use them in >> the version of JBrowse that I checked out from github. Neither >> branch (master or lazyfeatures) seems to be working. >> Specifically, when I add the "Ensembl Genes" track to the >> display, nothing is getting rendered. Also, is there any >> documentation as to how you were able to generate all of the >> trackData.json files? I know there is a set of perl scripts, >> but a more detailed tutorial (with example files) would be very >> useful. >> >> Thanks, >> Andrew Shinohara >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> |
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From: Mitch S. <mit...@be...> - 2010-04-28 23:48:46
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bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/ChromosomeBand.bed --tracklabel ChromosomeBand --key "Chromosome Band" --cssClass exon --getLabel --autoComplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CpGIslands.bed --tracklabel CpGIslands --key "CpG Islands" --cssClass basic --clientConfig '{"featureCss": "background-color: #0D0; height: 8px", "histCss": "background-color: #3D3"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/Gap.bed --tracklabel Gap --key "Gap" --cssClass --cssClass basic --clientConfig '{"featureCss": "background-color: #777; height: 8px", "histCss": "background-color: #777"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-daught-2878.bed --tracklabel "GenomeVariants-CEU-daught-2878" --key "GenomeVariants - CEU daught '2878" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/bacEndPairs.bed --tracklabel bacEndPairs --key "BAC End Pairs" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/EnsemblGenes.bed --tracklabel EnsemblGenes --key "Ensembl Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --autoComplete label --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-mother-2892.bed --tracklabel "GenomeVariants-CEU-mother-2892" --key "GenomeVariants - CEU mother '2892" --cssClass basic --clientConfig '{"featureCss": "background-color: #AF6; height: 8px", "histCss": "background-color: #BF8"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Venter.bed --tracklabel "GenomeVariants-Venter" --key "GenomeVariants - Venter" --cssClass basic --clientConfig '{"featureCss": "background-color: #FF00AF; height: 8px", "histCss": "background-color: #FF66CF"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Watson.bed --tracklabel "GenomeVariants-Watson" --key "GenomeVariants - Watson" --cssClass basic --clientConfig '{"featureCss": "background-color: #1834BA; height: 8px", "histCss": "background-color: #576DD9"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Yh1.bed --tracklabel "GenomeVariants-Yh1" --key "GenomeVariants - Yh1" --cssClass basic --clientConfig '{"featureCss": "background-color: #3D59CC; height: 8px", "histCss": "background-color: #5E79E6"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GWASCatalog.bed --tracklabel "GWASCatalog" --key "GWAS Catalog" --cssClass basic --clientConfig '{"featureCss": "background-color: #00F; height: 8px", "histCss": "background-color: #88F"}' --getLabel --autocomplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/HumanmRNAs-all_mrna.bed --tracklabel all_mrna --key "Human mRNAs" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --autoComplete label --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/MGCGenes.bed --tracklabel "MGCGenes" --key "MGC Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/N-SCAN.bed --tracklabel "N-SCAN" --key "N-SCAN" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/RefSeqGenes.bed --tracklabel "RefSeqGenes" --key "RefSeq Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs --autocomplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/STSMarkers.bed --tracklabel STSMarkers --key "STS Markers" --cssClass exon
history | grep flatfile-to-json | grep hg19-bed > ~/ff2json.txt
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CCDS.bed --tracklabel CCDS --key "Consensus CDS" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getLabel
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/Exoniphy.bed --tracklabel Exoniphy --key "Exoniphy" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CCDS.bed --tracklabel CCDS --key "Consensus CDS" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-father-2891.bed --tracklabel "GenomeVariants-CEU-father-2891" --key "GenomeVariants - CEU father '2891" --cssClass basic --clientConfig '{"featureCss": "background-color: #6F6; height: 8px", "histCss": "background-color: #8F8"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Sjk.bed --tracklabel "GenomeVariants-Sjk" --key "GenomeVariants - Sjk" --cssClass basic --clientConfig '{"featureCss": "background-color: #BA9843; height: 8px", "histCss": "background-color: #D4B56A"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/InterruptedRpts.bed --tracklabel InterruptedRpts --key "Interrupted Rpts" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/MapContigs.bed --tracklabel MapContigs --key "Map Contigs" --cssClass exon
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/OMIMGenes.bed --tracklabel OMIMGenes --key "OMIM Genes" --cssClass feature
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/ORFeomeClones.bed --tracklabel ORFeomeClones --key "ORFeome Clones" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SegmentalDups.bed --tracklabel SegmentalDups --key "Segmental Dups" --cssClass feature5
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SimpleRepeats.bed --tracklabel SimpleRepeats --key "Simple Repeats" --cssClass feature3
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-YRI-daught-9240.bed --tracklabel "GenomeVariants-YRI-daught-9240" --key "GenomeVariants - YRI daught '9240" --cssClass basic --clientConfig '{"featureCss": "background-color: #7245BB; height: 8px", "histCss": "background-color: #8F62D9"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SplicedESTs.bed --tracklabel SplicedESTs --key "Spliced ESTs" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
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From: Andrew S. <ac...@ge...> - 2010-04-29 14:14:19
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Mitch and Ian,
Thank you very much for the help! I am now up and running after
switching to that commit and generating my own JSON from the BED files
that UCSC provides.
Thanks again,
Andrew
On Wed, Apr 28, 2010 at 7:48 PM, Mitch Skinner
<mit...@be...> wrote:
> The human demo uses the "lazyfeatures" branch, but the demo hasn't been
> updated to the very latest code in that branch yet.
>
> If you want to use the json files from the human demo with the code from the
> human demo, use a slightly earlier version (commit 292aa08) of the
> lazyfeatures code. This is how I got there with git, there may be a more
> straightforward way to do this, but this is how I currently think of it:
> (this is what I did after the "git clone")
> ===============
> $ git branch
> * master
> $ git branch --track lazyfeatures origin/lazyfeatures
> Branch lazyfeatures set up to track remote branch
> refs/remotes/origin/lazyfeatures.
> $ git branch
> lazyfeatures
> * master
> $ git checkout lazyfeatures
> Switched to branch 'lazyfeatures'
> $ git checkout 292aa08
> Note: moving to '292aa08' which isn't a local branch
> If you want to create a new branch from this checkout, you may do so
> (now or later) by using -b with the checkout command again. Example:
> git checkout -b <new_branch_name>
> HEAD is now at 292aa08... actually set max_depth on all the writeJSON calls
> ===============
>
> Alternatively, you could download from here:
> http://github.com/jbrowse/jbrowse/archives/292aa081c37525fbf655bb99b60e466938b985bc
>
> Generally speaking, the demos aren't always using the very latest code
> because I'm often debugging the very latest code and the demos are meant to
> be a little more stable. So I usually expect that people will want to
> generate their own json files. If you want to do that, I've attached a list
> of the commands I used to generate the human demo. It's not complete; it's
> just what I still have in my shell command history. But hopefully it gives
> you a sense of how to use flatfile-to-json.pl.
>
> The attached list of commands uses BED files that I downloaded from the UCSC
> table browser as input. Sometime soon, I'll implement a more convenient way
> of setting up a JBrowse instance from UCSC data, but currently the best
> thing to do is use BED files.
>
> Also, (with the current code) the larger tracks often work better if they're
> split up by chromosome, e.g. (using bash):
>
> ===============
> pushd ~/data/ucsc/hg19-bed
> for x in `seq 1 22` X Y; do grep "^chr$x"$'\t' SplicedESTs.bed >
> SplicedESTs-chr$x.bed; done
> popd
> for x in `seq 22 -1 1` X Y; do bin/flatfile-to-json.pl --bed
> ~/data/ucsc/hg19-bed/SplicedESTs-chr$x.bed --tracklabel SplicedESTs --key
> "Spliced ESTs" --cssClass generic_parent --subfeatureClasses '{"CDS":
> "match_part"}' --getSubs; done
> ===============
>
> But if you have enough RAM you may not need to do that.
>
> Hope this helps,
> Mitch
>
> On 04/28/2010 08:38 AM, Andrew Shinohara wrote:
>
> Hello,
> I am viewing the tracks on the JBrowse demo site at
> http://jbrowse.org/ucsc/hg19/ and have a couple of questions. What version
> of JBrowse is this using? I have attempted to take the trackData.json files
> from the demo site and use them in the version of JBrowse that I checked out
> from github. Neither branch (master or lazyfeatures) seems to be working.
> Specifically, when I add the "Ensembl Genes" track to the display, nothing
> is getting rendered. Also, is there any documentation as to how you were
> able to generate all of the trackData.json files? I know there is a set of
> perl scripts, but a more detailed tutorial (with example files) would be
> very useful.
>
> Thanks,
> Andrew Shinohara
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
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