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From: Philippe B. <phi...@to...> - 2010-07-01 14:44:43
|
Hi all,
I'm trying to include jbrowse in our "rich" web application.
To do that, I need to "display:none" the jbrowse div but some display bugs appear ?
At start I thought that my problem cames from conflict with jquery but finaly not.
<body>
<span onclick="if(document.getElementById('GenomeBrowser').style.display=='none') {document.getElementById('GenomeBrowser').style.display='block';} else {document.getElementById('GenomeBrowser').style.display='none';}">
Click Me
</span>
<div id="GenomeBrowser" style="display: none; height: 100%; width: 100%; padding: 0; border: 0;"></div>
</body>
If I start without "display: none;" all works fine but it is not what I need...
Hope I'm clear... ?
Thanks for your reply
Philippe
PS : Thanks a lot Andrew and Mich for your previous replies...!
> Philippe,
> We ran into a similar issue as we are using jQuery in our
> application as well as JBrowse. You may not need to embed an iframe.
> Take a look at the noConflict method of jQuery:
>
> http://api.jquery.com/jQuery.noConflict/
>
> This allowed us to use jQuery and JBrowse.
>
> -Andrew
>
> On Thu, Jul 1, 2010 at 4:04 AM, Philippe Bardou
> <phi...@to...
> <mailto:phi...@to...>> wrote:
>
> Hi,
>
> Due to jquery in our website I'm trying to embed JBrowse in an iframe.
> It works fine with google-chrome but nothing happens, nothing
> appears with IE8 and Firefox3.6.6.
> Do you have any idea ?
>
> Thanks a lot for your help
>
> Philippe
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first <http://sprint.com/first> --
> http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Mitch S. <mit...@be...> - 2010-07-01 14:27:49
|
Hi, I've seen this but I haven't yet figured out exactly what's going on. I think it has something to do with paired-end reads, and it might be caused by reads whose pair-mate isn't mapped. Handling paired-end reads better is something I'm currently working on. Mitch On 06/23/2010 01:35 AM, sanjay shah wrote: > Hi , > > > Sorry Typo error in the earlier mail .. > > The bam file is "20100311.sorted.bam" and not "20100311.bam" > that is being provided in the command after index has been created as > : > " 20100311.sorted.bam.bai .".. > So the command executed is : > $$ bin/flatfile-to-json.pl --bam > /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon > --tracklabel BAM_data --key "BAM Data" > > > which throws the following error > > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > > > please help ..Thanks > > Thanks, > Sanjay > > > > > Thanks, > Sanjay > > On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<bea...@gm...> wrote: > >> Hi , >> >> Thanks.I did sort the alignments and then created index manually >> with samtools( I have "20100311.sorted.bam.bai " file ) ; now when I >> again try to convert BAM to JSON by issuing command as: >> >> >> $$ bin/flatfile-to-json.pl --bam >> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >> --tracklabel BAM_data --key "BAM Data" >> >> >> I get following error: >> >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> >> >> >> Please help on this aspect ..Thanks >> >> >> Thanks, >> Sanjay >> >> >> On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner >> <mit...@be...> wrote: >> >>> In the future, JBrowse will probably use the autoindexing option as >>> suggested by that error message. >>> >>> Right now, though, you can get around this by creating the index manually >>> with samtools; you'd write something like: >>> >>> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam >>> >>> (using the full path to the samtools program if it's not in your path) >>> >>> Mitch >>> >>> On 06/22/2010 02:12 AM, sanjay shah wrote: >>> >>>> Hi, >>>> >>>> I have a BAM file and when i execute the following command to >>>> convert the BAM to Json : >>>> >>>> $$ bin/flatfile-to-json.pl --bam >>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >>>> --tracklabel BAM_data --key "BAM Data" >>>> >>>> I get the following error; >>>> >>>> No index file for >>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening >>>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line >>>> 1940 >>>> >>>> I have installed the prerequisite installed for browsing BAM files in >>>> Jbrowse .I also have the corresponding reference file in Json and am >>>> able to browse in Jbrowse. >>>> >>>> >>>> Do we have to create any index for browsing BAM files in Jbrowse >>>> before we convert it to Json .Please help me in resolving the >>>> following error. >>>> >>>> >>>> >>>> Thanks, >>>> Sanjay >>>> >>>> >>>> >>> >>> >> >> >> -- >> Success is how many times u smile each day every day. >> >> > > > |
|
From: Mitch S. <mit...@be...> - 2010-07-01 14:23:52
|
On 07/01/2010 06:27 AM, Andrew Shinohara wrote: > Philippe, > We ran into a similar issue as we are using jQuery in our > application as well as JBrowse. You may not need to embed an iframe. > Take a look at the noConflict method of jQuery: > > http://api.jquery.com/jQuery.noConflict/ > > This allowed us to use jQuery and JBrowse. Thanks for pointing this out. I did remove the conflicting $ function from JBrowse last December in response to Jerome Mariette's comment back then: http://github.com/jbrowse/jbrowse/commit/ed13ddeb11dd28137c6d3c3022fe38e42efdf6d1 and I was hoping that would allow jQuery and JBrowse to coexist without requiring jQuery.noConflict. Philippe: > Due to jquery in our website I'm trying to embed JBrowse in an iframe. > It works fine with google-chrome but nothing happens, nothing appears with IE8 and Firefox3.6.6. > Do you have any idea ? Did you try to embed without an iframe? I do think JBrowse ought to work in an iframe as well; does it work if you navigate to the page directly (not in an iframe)? If that works, then I don't know why it wouldn't work inside an iframe. Mitch |
|
From: Andrew S. <ash...@gm...> - 2010-07-01 13:27:52
|
Philippe,
We ran into a similar issue as we are using jQuery in our application as
well as JBrowse. You may not need to embed an iframe. Take a look at the
noConflict method of jQuery:
http://api.jquery.com/jQuery.noConflict/
This allowed us to use jQuery and JBrowse.
-Andrew
On Thu, Jul 1, 2010 at 4:04 AM, Philippe Bardou <
phi...@to...> wrote:
> Hi,
>
> Due to jquery in our website I'm trying to embed JBrowse in an iframe.
> It works fine with google-chrome but nothing happens, nothing appears with
> IE8 and Firefox3.6.6.
> Do you have any idea ?
>
> Thanks a lot for your help
>
> Philippe
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Philippe B. <phi...@to...> - 2010-07-01 08:04:16
|
Hi, Due to jquery in our website I'm trying to embed JBrowse in an iframe. It works fine with google-chrome but nothing happens, nothing appears with IE8 and Firefox3.6.6. Do you have any idea ? Thanks a lot for your help Philippe |
|
From: Mariette <jma...@to...> - 2010-07-01 08:00:16
|
Thanks Mitch for your reply, it's working the probleme was coming from the path of the 'seqDir' and the path of the 'url' fields which were not absolute from the calling page. Thanks again, Jerome Mitch Skinner a écrit : > JBrowse doesn't use the directory listings; when JBrowse gets a file > from the server it's through a direct link (or a URL template, in some > places). > > It's harder to debug if I can't see the app, but my first guess would be > that it has something to do with relative URLs. refSeq.js and > trackInfo.js both contain URLs relative to the directory containing the > jbrowse index.html file. > > That's assuming that you're using the default index.html file. Are you > doing that, or are you doing something else? > > There's a setting (the "dataRoot" parameter to the Browser javascript > object constructor) that makes the root of those relative URLs > configurable, but because of a recent exchange on the gmod-ajax list I'm > looking at changing how that works. If you've got a non-default > directory setup I'd be interested to know how you have things laid out, > so that we can make sure that setting works correctly for everyone. > > Regards, > Mitch > > On 06/30/2010 06:06 AM, Mariette wrote: > >> Hi, >> >> I'm trying to get jbrowse runing into our website. However it's not working, >> I have the jbrowse environement displayed but not annotations and the >> seqRef. >> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the >> 'seqDir' and >> the 'url' fields of these files. >> We figured out that the jbrowse sample web site allows to list files >> into directories. >> Is it required to make jbrowse working ?? >> The problem is we're using the cherrypy web server which doesn't seems >> to allow >> files listing, and we're guessing this is the problem ? would that make >> sens ?? >> >> thanks for your reply, >> Jerome >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Mitch S. <mit...@be...> - 2010-06-30 23:46:03
|
On 06/30/2010 04:44 PM, Mitch Skinner wrote: > There's a setting (the "dataRoot" parameter to the Browser javascript > object constructor) > I forgot to add, there's a bit of documentation on those parameters here: http://jbrowse.org/docs/jbrowse-jsdoc/symbols/Browser.html Mitch |
|
From: Mitch S. <mit...@be...> - 2010-06-30 23:44:31
|
JBrowse doesn't use the directory listings; when JBrowse gets a file from the server it's through a direct link (or a URL template, in some places). It's harder to debug if I can't see the app, but my first guess would be that it has something to do with relative URLs. refSeq.js and trackInfo.js both contain URLs relative to the directory containing the jbrowse index.html file. That's assuming that you're using the default index.html file. Are you doing that, or are you doing something else? There's a setting (the "dataRoot" parameter to the Browser javascript object constructor) that makes the root of those relative URLs configurable, but because of a recent exchange on the gmod-ajax list I'm looking at changing how that works. If you've got a non-default directory setup I'd be interested to know how you have things laid out, so that we can make sure that setting works correctly for everyone. Regards, Mitch On 06/30/2010 06:06 AM, Mariette wrote: > Hi, > > I'm trying to get jbrowse runing into our website. However it's not working, > I have the jbrowse environement displayed but not annotations and the > seqRef. > Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the > 'seqDir' and > the 'url' fields of these files. > We figured out that the jbrowse sample web site allows to list files > into directories. > Is it required to make jbrowse working ?? > The problem is we're using the cherrypy web server which doesn't seems > to allow > files listing, and we're guessing this is the problem ? would that make > sens ?? > > thanks for your reply, > Jerome > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Giles V. <gv...@sa...> - 2010-06-30 15:04:17
|
That does make sense. Will be interesting to see if the cherrypy static dir index will work with JBrowse. If it doesn't, then I would suggest writing a mock-index controller in CherryPy yourself, essentially returning the same thing that JBrowse is expecting. In theory, all you would have to do is write an exposed method that lists the contents of a directory, formatting this appropriately, and map it to requests that the JBrowse javascript is making. Regards, Giles On 30 Jun 2010, at 15:37, Mariette wrote: > > Thanks, > > I will take a look. I'm deploying jbrowse on cherrypy > because the application we're developing is deploying > on cherrypy and I want jbrowse to be embeded into > our application. So I don't want jbrowse to be outside > of the application itself. > > does it make sense ? > > Jerome > > > > > > > > > > Giles Velarde a écrit : >> Hi, >> >> Perhaps I should respond here because I do use CherryPy for some >> projects, and use JBrowse in another. I would look at >> >> http://tools.cherrypy.org/wiki/staticdirindex >> >> and see if that helps you (I haven't tried this myself). >> >> That said, why are you deploying JBrowse on CherryPy and not >> Apache? JBrowse needs the web server to only serve static pre- >> generated JSON files, and Apache works perfectly well for that. If >> the data sets get fairly large, you may find any server other than >> Apache may well struggle to cope. >> >> If you need to run some other server-side dynamic pages in Python, >> you can always put CherryPy behind the same Apache server as well. >> See >> >> http://tools.cherrypy.org/wiki/BehindApache >> >> for more info. >> >> Regards, >> Giles >> >> >> On 30 Jun 2010, at 14:06, Mariette wrote: >> >> >>> Hi, >>> >>> I'm trying to get jbrowse runing into our website. However it's >>> not working, >>> I have the jbrowse environement displayed but not annotations and >>> the >>> seqRef. >>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't >>> read the >>> 'seqDir' and >>> the 'url' fields of these files. >>> We figured out that the jbrowse sample web site allows to list files >>> into directories. >>> Is it required to make jbrowse working ?? >>> The problem is we're using the cherrypy web server which doesn't >>> seems >>> to allow >>> files listing, and we're guessing this is the problem ? would >>> that make >>> sens ?? >>> >>> thanks for your reply, >>> Jerome >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by Sprint >>> What will you do first with EVO, the first 4G phone? >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> >> >> >> > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
|
From: Mariette <jma...@to...> - 2010-06-30 14:37:42
|
Thanks, I will take a look. I'm deploying jbrowse on cherrypy because the application we're developing is deploying on cherrypy and I want jbrowse to be embeded into our application. So I don't want jbrowse to be outside of the application itself. does it make sense ? Jerome Giles Velarde a écrit : > Hi, > > Perhaps I should respond here because I do use CherryPy for some > projects, and use JBrowse in another. I would look at > > http://tools.cherrypy.org/wiki/staticdirindex > > and see if that helps you (I haven't tried this myself). > > That said, why are you deploying JBrowse on CherryPy and not Apache? > JBrowse needs the web server to only serve static pre-generated JSON > files, and Apache works perfectly well for that. If the data sets get > fairly large, you may find any server other than Apache may well > struggle to cope. > > If you need to run some other server-side dynamic pages in Python, you > can always put CherryPy behind the same Apache server as well. See > > http://tools.cherrypy.org/wiki/BehindApache > > for more info. > > Regards, > Giles > > > On 30 Jun 2010, at 14:06, Mariette wrote: > > >> Hi, >> >> I'm trying to get jbrowse runing into our website. However it's not >> working, >> I have the jbrowse environement displayed but not annotations and the >> seqRef. >> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read >> the >> 'seqDir' and >> the 'url' fields of these files. >> We figured out that the jbrowse sample web site allows to list files >> into directories. >> Is it required to make jbrowse working ?? >> The problem is we're using the cherrypy web server which doesn't seems >> to allow >> files listing, and we're guessing this is the problem ? would that >> make >> sens ?? >> >> thanks for your reply, >> Jerome >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > > > > |
|
From: Giles V. <gv...@sa...> - 2010-06-30 14:29:06
|
Hi, Perhaps I should respond here because I do use CherryPy for some projects, and use JBrowse in another. I would look at http://tools.cherrypy.org/wiki/staticdirindex and see if that helps you (I haven't tried this myself). That said, why are you deploying JBrowse on CherryPy and not Apache? JBrowse needs the web server to only serve static pre-generated JSON files, and Apache works perfectly well for that. If the data sets get fairly large, you may find any server other than Apache may well struggle to cope. If you need to run some other server-side dynamic pages in Python, you can always put CherryPy behind the same Apache server as well. See http://tools.cherrypy.org/wiki/BehindApache for more info. Regards, Giles On 30 Jun 2010, at 14:06, Mariette wrote: > Hi, > > I'm trying to get jbrowse runing into our website. However it's not > working, > I have the jbrowse environement displayed but not annotations and the > seqRef. > Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read > the > 'seqDir' and > the 'url' fields of these files. > We figured out that the jbrowse sample web site allows to list files > into directories. > Is it required to make jbrowse working ?? > The problem is we're using the cherrypy web server which doesn't seems > to allow > files listing, and we're guessing this is the problem ? would that > make > sens ?? > > thanks for your reply, > Jerome > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
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From: Mariette <jma...@to...> - 2010-06-30 13:06:34
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Hi, I'm trying to get jbrowse runing into our website. However it's not working, I have the jbrowse environement displayed but not annotations and the seqRef. Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the 'seqDir' and the 'url' fields of these files. We figured out that the jbrowse sample web site allows to list files into directories. Is it required to make jbrowse working ?? The problem is we're using the cherrypy web server which doesn't seems to allow files listing, and we're guessing this is the problem ? would that make sens ?? thanks for your reply, Jerome |
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From: Ian H. <ih...@be...> - 2010-06-30 01:55:42
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Hi Swapnil, If you click on the "Link" at the top right of the page, JBrowse will create a bookmark URL that reveals the general form you want, e.g. http://jbrowse.org/ucsc/hg19/?loc=chr1:99700248..149550372&tracks=DNA Best wishes, Ian Swapnil Nagar wrote: > Hi, > > We are presently working on Jbrowse. We want to connect the our Ncbi Blast with the Jbrowse. So for this purpose we need to know about, how to look at some specific position in JBrowse with specific enabled tracks (I mean here is URL). Can I prepare the dynamic URL (like in Gbrowse) in Jbrowse and display desired position ? > > Thanks, > > Swapnil > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Swapnil N. <zea...@k-...> - 2010-06-29 18:59:16
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Hi, We are presently working on Jbrowse. We want to connect the our Ncbi Blast with the Jbrowse. So for this purpose we need to know about, how to look at some specific position in JBrowse with specific enabled tracks (I mean here is URL). Can I prepare the dynamic URL (like in Gbrowse) in Jbrowse and display desired position ? Thanks, Swapnil |
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From: sanjay s. <bea...@gm...> - 2010-06-23 08:35:31
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Hi , Sorry Typo error in the earlier mail .. The bam file is "20100311.sorted.bam" and not "20100311.bam" that is being provided in the command after index has been created as : " 20100311.sorted.bam.bai .".. So the command executed is : $$ bin/flatfile-to-json.pl --bam /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon --tracklabel BAM_data --key "BAM Data" which throws the following error Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. please help ..Thanks Thanks, Sanjay Thanks, Sanjay On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah <bea...@gm...> wrote: > Hi , > > Thanks.I did sort the alignments and then created index manually > with samtools( I have "20100311.sorted.bam.bai " file ) ; now when I > again try to convert BAM to JSON by issuing command as: > > > $$ bin/flatfile-to-json.pl --bam > /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon > --tracklabel BAM_data --key "BAM Data" > > > I get following error: > > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > > > > Please help on this aspect ..Thanks > > > Thanks, > Sanjay > > > On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner > <mit...@be...> wrote: >> In the future, JBrowse will probably use the autoindexing option as >> suggested by that error message. >> >> Right now, though, you can get around this by creating the index manually >> with samtools; you'd write something like: >> >> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam >> >> (using the full path to the samtools program if it's not in your path) >> >> Mitch >> >> On 06/22/2010 02:12 AM, sanjay shah wrote: >>> >>> Hi, >>> >>> I have a BAM file and when i execute the following command to >>> convert the BAM to Json : >>> >>> $$ bin/flatfile-to-json.pl --bam >>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >>> --tracklabel BAM_data --key "BAM Data" >>> >>> I get the following error; >>> >>> No index file for >>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening >>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line >>> 1940 >>> >>> I have installed the prerequisite installed for browsing BAM files in >>> Jbrowse .I also have the corresponding reference file in Json and am >>> able to browse in Jbrowse. >>> >>> >>> Do we have to create any index for browsing BAM files in Jbrowse >>> before we convert it to Json .Please help me in resolving the >>> following error. >>> >>> >>> >>> Thanks, >>> Sanjay >>> >>> >> >> > > > > -- > Success is how many times u smile each day every day. > -- Success is how many times u smile each day every day. |
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From: sanjay s. <bea...@gm...> - 2010-06-23 08:25:40
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Hi , Thanks.I did sort the alignments and then created index manually with samtools( I have "20100311.sorted.bam.bai " file ) ; now when I again try to convert BAM to JSON by issuing command as: $$ bin/flatfile-to-json.pl --bam /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon --tracklabel BAM_data --key "BAM Data" I get following error: Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Please help on this aspect ..Thanks Thanks, Sanjay On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner <mit...@be...> wrote: > In the future, JBrowse will probably use the autoindexing option as > suggested by that error message. > > Right now, though, you can get around this by creating the index manually > with samtools; you'd write something like: > > $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam > > (using the full path to the samtools program if it's not in your path) > > Mitch > > On 06/22/2010 02:12 AM, sanjay shah wrote: >> >> Hi, >> >> I have a BAM file and when i execute the following command to >> convert the BAM to Json : >> >> $$ bin/flatfile-to-json.pl --bam >> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >> --tracklabel BAM_data --key "BAM Data" >> >> I get the following error; >> >> No index file for >> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening >> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line >> 1940 >> >> I have installed the prerequisite installed for browsing BAM files in >> Jbrowse .I also have the corresponding reference file in Json and am >> able to browse in Jbrowse. >> >> >> Do we have to create any index for browsing BAM files in Jbrowse >> before we convert it to Json .Please help me in resolving the >> following error. >> >> >> >> Thanks, >> Sanjay >> >> > > -- Success is how many times u smile each day every day. |
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From: Mitch S. <mit...@be...> - 2010-06-22 13:08:01
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In the future, JBrowse will probably use the autoindexing option as suggested by that error message. Right now, though, you can get around this by creating the index manually with samtools; you'd write something like: $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam (using the full path to the samtools program if it's not in your path) Mitch On 06/22/2010 02:12 AM, sanjay shah wrote: > Hi, > > I have a BAM file and when i execute the following command to > convert the BAM to Json : > > $$ bin/flatfile-to-json.pl --bam > /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon > --tracklabel BAM_data --key "BAM Data" > > I get the following error; > > No index file for > /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening > file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line > 1940 > > I have installed the prerequisite installed for browsing BAM files in > Jbrowse .I also have the corresponding reference file in Json and am > able to browse in Jbrowse. > > > Do we have to create any index for browsing BAM files in Jbrowse > before we convert it to Json .Please help me in resolving the > following error. > > > > Thanks, > Sanjay > > |
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From: sanjay s. <bea...@gm...> - 2010-06-22 09:12:36
|
Hi, I have a BAM file and when i execute the following command to convert the BAM to Json : $$ bin/flatfile-to-json.pl --bam /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon --tracklabel BAM_data --key "BAM Data" I get the following error; No index file for /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line 1940 I have installed the prerequisite installed for browsing BAM files in Jbrowse .I also have the corresponding reference file in Json and am able to browse in Jbrowse. Do we have to create any index for browsing BAM files in Jbrowse before we convert it to Json .Please help me in resolving the following error. Thanks, Sanjay -- Success is how many times u smile each day every day. |
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From: sanjay s. <bea...@gm...> - 2010-06-16 04:17:50
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Hi,
Thanks Ian.I have installed make and g++ and it works fine now.
Thank you so much .
Regards,
Sanjay
On Tue, Jun 15, 2010 at 9:43 PM, Ian Holmes <ih...@be...> wrote:
> It sounds like your system does not have the 'make' tool installed. In order
> to build the wig2png program you need developer tools (make, gcc). What
> hardware/OS/version are you using?
>
> sanjay shah wrote:
>>
>> Hi ,
>>
>> Thanks.Am just trying to browse quantitative ("wiggle") tracks in
>> JBrowse.There is a sample wig file available under
>> /tutorial/data_files and am trying to use the same .The steps from
>> terminal are as below:
>>
>>
>> @:/var/www/jbrowse$ bin/wig-to-json.pl --wig
>> docs/tutorial/data_files/volvox_microarray.wig
>> Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing
>> 'make' in jbrowse root directory?) at bin/wig-to-json.pl line 28.
>>
>>
>> Now when I type make from the root directory it says no command found:
>>
>>
>> @/var/www/jbrowse$ make
>> -bash: make: command not found
>>
>> Now when i list all the files in the root directory of Jbrowse with
>> :ls -ltr i cannot find any make file there .
>>
>>
>> How could i compile "src/wig2png.cc" to browse wiggle tracks
>> then?Could you please help on this one...?
>>
>>
>> Thanks,
>> Sanjay
>>
>>
>> On Tue, Jun 15, 2010 at 2:17 PM, Mitch Skinner
>> <mit...@be...> wrote:
>>>
>>> Hi,
>>>
>>> Could you be more specific about what you're doing, and what you're
>>> seeing?
>>> If you could go into your terminal and copy and paste from there into an
>>> email, including the commands you ran, and the output you saw, that would
>>> be
>>> very helpful for understanding what's happening.
>>>
>>> Mitch
>>>
>>> On 06/14/2010 03:03 AM, sanjay shah wrote:
>>>>
>>>> Hi ,
>>>>
>>>> I jus tdownloaded Jbrowse form git and then trying to use it .
>>>> Am trying Jbrowse for Quantitative tracks and as to go by docs :
>>>> i first need to Compile the wiggle-processing program by running make
>>>> in the JBrowse root directory
>>>> So when i do :
>>>>
>>>> make
>>>>
>>>> It throws error make command file .I do not find make file in the
>>>> root ..Could you help me on this?How do i go about it ?
>>>>
>>>> Thanks,
>>>> Sanjay
>>>>
>>>>
>>>
>>
>>
>>
>
--
Success is how many times u smile each day every day.
|
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From: Ian H. <ih...@be...> - 2010-06-15 15:58:15
|
It sounds like your system does not have the 'make' tool installed. In
order to build the wig2png program you need developer tools (make, gcc).
What hardware/OS/version are you using?
sanjay shah wrote:
> Hi ,
>
> Thanks.Am just trying to browse quantitative ("wiggle") tracks in
> JBrowse.There is a sample wig file available under
> /tutorial/data_files and am trying to use the same .The steps from
> terminal are as below:
>
>
> @:/var/www/jbrowse$ bin/wig-to-json.pl --wig
> docs/tutorial/data_files/volvox_microarray.wig
> Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing
> 'make' in jbrowse root directory?) at bin/wig-to-json.pl line 28.
>
>
> Now when I type make from the root directory it says no command found:
>
>
> @/var/www/jbrowse$ make
> -bash: make: command not found
>
> Now when i list all the files in the root directory of Jbrowse with
> :ls -ltr i cannot find any make file there .
>
>
> How could i compile "src/wig2png.cc" to browse wiggle tracks
> then?Could you please help on this one...?
>
>
> Thanks,
> Sanjay
>
>
> On Tue, Jun 15, 2010 at 2:17 PM, Mitch Skinner
> <mit...@be...> wrote:
>> Hi,
>>
>> Could you be more specific about what you're doing, and what you're seeing?
>> If you could go into your terminal and copy and paste from there into an
>> email, including the commands you ran, and the output you saw, that would be
>> very helpful for understanding what's happening.
>>
>> Mitch
>>
>> On 06/14/2010 03:03 AM, sanjay shah wrote:
>>> Hi ,
>>>
>>> I jus tdownloaded Jbrowse form git and then trying to use it .
>>> Am trying Jbrowse for Quantitative tracks and as to go by docs :
>>> i first need to Compile the wiggle-processing program by running make
>>> in the JBrowse root directory
>>> So when i do :
>>>
>>> make
>>>
>>> It throws error make command file .I do not find make file in the
>>> root ..Could you help me on this?How do i go about it ?
>>>
>>> Thanks,
>>> Sanjay
>>>
>>>
>>
>
>
>
|
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From: sanjay s. <bea...@gm...> - 2010-06-15 10:00:15
|
Hi ,
Thanks.Am just trying to browse quantitative ("wiggle") tracks in
JBrowse.There is a sample wig file available under
/tutorial/data_files and am trying to use the same .The steps from
terminal are as below:
@:/var/www/jbrowse$ bin/wig-to-json.pl --wig
docs/tutorial/data_files/volvox_microarray.wig
Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing
'make' in jbrowse root directory?) at bin/wig-to-json.pl line 28.
Now when I type make from the root directory it says no command found:
@/var/www/jbrowse$ make
-bash: make: command not found
Now when i list all the files in the root directory of Jbrowse with
:ls -ltr i cannot find any make file there .
How could i compile "src/wig2png.cc" to browse wiggle tracks
then?Could you please help on this one...?
Thanks,
Sanjay
On Tue, Jun 15, 2010 at 2:17 PM, Mitch Skinner
<mit...@be...> wrote:
> Hi,
>
> Could you be more specific about what you're doing, and what you're seeing?
> If you could go into your terminal and copy and paste from there into an
> email, including the commands you ran, and the output you saw, that would be
> very helpful for understanding what's happening.
>
> Mitch
>
> On 06/14/2010 03:03 AM, sanjay shah wrote:
>>
>> Hi ,
>>
>> I jus tdownloaded Jbrowse form git and then trying to use it .
>> Am trying Jbrowse for Quantitative tracks and as to go by docs :
>> i first need to Compile the wiggle-processing program by running make
>> in the JBrowse root directory
>> So when i do :
>>
>> make
>>
>> It throws error make command file .I do not find make file in the
>> root ..Could you help me on this?How do i go about it ?
>>
>> Thanks,
>> Sanjay
>>
>>
>
>
--
Success is how many times u smile each day every day.
|
|
From: Mitch S. <mit...@be...> - 2010-06-15 08:32:20
|
Hi, Could you be more specific about what you're doing, and what you're seeing? If you could go into your terminal and copy and paste from there into an email, including the commands you ran, and the output you saw, that would be very helpful for understanding what's happening. Mitch On 06/14/2010 03:03 AM, sanjay shah wrote: > Hi , > > I jus tdownloaded Jbrowse form git and then trying to use it . > Am trying Jbrowse for Quantitative tracks and as to go by docs : > i first need to Compile the wiggle-processing program by running make > in the JBrowse root directory > So when i do : > > make > > It throws error make command file .I do not find make file in the > root ..Could you help me on this?How do i go about it ? > > Thanks, > Sanjay > > |
|
From: sanjay s. <bea...@gm...> - 2010-06-14 10:04:04
|
Hi , I jus tdownloaded Jbrowse form git and then trying to use it . Am trying Jbrowse for Quantitative tracks and as to go by docs : i first need to Compile the wiggle-processing program by running make in the JBrowse root directory So when i do : make It throws error make command file .I do not find make file in the root ..Could you help me on this?How do i go about it ? Thanks, Sanjay -- Success is how many times u smile each day every day. |
|
From: Mitch S. <mit...@be...> - 2010-06-07 18:25:29
|
On 06/07/2010 05:47 AM, James Casbon wrote: > > Is the JSON data format that JBrowse uses stable enough that it is > worth creating my own JSON, or do you anticipate it changing it? > Could it represent an interface to the program, or is it an internal > only part? > > Sorry for the slow reply. The short answer is, the feature JSON was just an internal interface, but you've caught me right in the middle of thinking about whether and how to make it an external interface. I originally wanted it to be just an internal interface for a couple of reasons: 1. it was changing a lot, and 2. there are already so many genomics file formats; I would have felt guilty about making another one. However, things have changed a bit: 1. it's no longer changing quite as much 2. it may be possible to separate the parts that I expect to change from the parts that probably won't change 3. web browsers impose their own set of limitations that I think may justify having a new format 4. people keep asking for it So now I'm thinking that we should probably do as you're asking, with the caveat that I haven't yet separated the likely-to-change bits from the unlikely-to-change bits. And there's not a perfectly clear-cut boundary between those things. The feature JSON currently contains: 1. feature data 2. feature density histogram counts 3. information on how to visually present the features, and 4. a bunch of parameters that tell the client how to behave (e.g., the zoom threshold where the client switches from showing feature density histograms to showing actual features) I'm think #1 and #2 are pretty stable, and #4 is very likely to change. But I'm not sure about #3. So I'd be comfortable with describing and documenting #1 and #2 and having that be an external interface. But right now all those things are combined together in one file. Also, that documentation still has to be written. I've got a very incomplete start here: http://biowiki.org/view/JBrowse/JSONFeatureFormat I've also got a paper deadline coming up very soon, so it may be a little while before that documentation is fully fleshed out. I'll send a message to gmod-ajax when it's more complete. Or, if you're really keen, you could, of course, look at the code and the generated files to get a more direct view of it. I could certainly answer questions about what's in there and why. Mitch |
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From: James C. <ca...@gm...> - 2010-06-07 12:47:05
|
On 3 June 2010 09:50, James Casbon <ca...@gm...> wrote: > I really like using jbrowse, but one thing I don't like is having to > use bioperl to produce the JSON structures. Would you consider > publishing a brief spec of the JSON expected by jbrowse so that I can > consider publishing my own JSON nested lists? No response, so I'll try this instead... Is the JSON data format that JBrowse uses stable enough that it is worth creating my own JSON, or do you anticipate it changing it? Could it represent an interface to the program, or is it an internal only part? thanks, James |
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