gmod-ajax — JBrowse list

Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[Scott C. <sc...@sc...>]

Hi David,

The NCBI GFF3 is notoriously bad and doesn't pass validation at the
GFF3 validator:

  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

The most notable problems actually have to do with the relationships
between features.  For example, in the first few lines:

NC_007777.1     RefSeq  gene    35      1723    .       +       .
 locus_tag=Francci3_0001;db_xref=GeneID:3902947
NC_007777.1     RefSeq  CDS     35      1720    .       +       0
 locus_tag=Francci3_0001;transl_table=11;product=chromosomal
replication initiator protein
DnaA;protein_id=YP_479125.1;db_xref=GI:86738725;db_xref=InterPro:IPR001957;db_xref=InterPro:IPR003593;db_xref=InterPro:IPR013159;db_xref=InterPro:IPR013317;db_xref=GeneID:3902947;exon_number=1

While there is not anything technically wrong with these two lines,
there is what you might call a logic error: the CDS should have the
gene as a parent.  Without that information, a genome browser is going
to have a difficult time displaying the data appropriately.  Feel free
to complain to the folks at NCBI that there GFF3 is really bad (I've
done that a few times, but I think they are ignoring me :-)

So, the question is, what should you use?  The best option I can
suggest to you is the genbank2gff3 script that comes with BioPerl,
called bp_genbank2gff3.pl. If you get the developers version from
github, you can use a version of that script that has been fixed to
work appropriately with bacterial/circular genomes.

Scott


On Fri, Jul 23, 2010 at 10:54 AM, David Breimann
<dav...@gm...> wrote:
> I am trying to set up my first genome, after successfully playing with
> the tutorial examples. and I run into some problems.
>
> I use a fasta and a gff file from NCBI:
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
>
> Setting up the sequence file seems to pass OK, but when I run
> flatfile-to-json.pl with the GFF I get an error:
>
>
> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
> --tracklabel test -key test
>
> working on seq gi|86738724|ref|NC_007777.1|
> Use of uninitialized value in string eq at
> ../../../jbrowse/bin/flatfile-to-json.pl line 179, <GEN2> line 24.
>
> What's wrong?
>
> Thank you,
> David
>
> ------------------------------------------------------------------------------
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] flatfile-to-json.pl error with GFF

[David B. <dav...@gm...>]

I am trying to set up my first genome, after successfully playing with
the tutorial examples. and I run into some problems.

I use a fasta and a gff file from NCBI:
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff

Setting up the sequence file seems to pass OK, but when I run
flatfile-to-json.pl with the GFF I get an error:


../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
--tracklabel test -key test

working on seq gi|86738724|ref|NC_007777.1|
Use of uninitialized value in string eq at
../../../jbrowse/bin/flatfile-to-json.pl line 179, <GEN2> line 24.

What's wrong?

Thank you,
David

[Gmod-ajax] Define boundary in DNA Fasta sequence

[Swapnil N. <zea...@k-...>]

Hi,

I have successfully put the DNA sequence in the Jbrowse. We were hoping that like we define the gene boundary for Mrna, Can we do same for the DNA (fasta sequence)? It would be really nice if jbrowse enable us to highlight the biological classes(5' UTR, 3'UTR, exon, intron, etc) in different color.

Thanks,

Swapnil Nagar

[Gmod-ajax] Using multiple "data" directories with a single copy of JBrowse code

[Mitch S. <mit...@be...>]

A lot of people have been asking about this lately, and it's something I 
hadn't looked at in a while so it took me some time to remember all the 
details.  Now that I do, I wanted to write a message that hopefully 
helps all of the people asking about this.  This should also address the 
issues some people were having with relative URLs.

First of all, if you only have a few JBrowse instances ("instance" 
meaning "data set", e.g. a genome) , it's probably easiest to just have 
a separate copy of JBrowse for each one.  And, right now, that's the 
recommended approach: just make copies, and ignore the rest of this 
email.  Now that this is becoming such a common request, I plan to 
streamline things in a future version, but right now you have to do 
things in a very specific way for it to work.

If you have a lot of different JBrowse instances, though, or if  you 
want to create new ones on the fly, then read on:

Each instance needs to be in a directory named "data", and that 
directory needs to be in a directory with a unique path.  So, for 
example, if you have two genomes, genome1 and genome2, the directory 
setup should look like this:

genome1/
    data/
genome2/
    data/

Suppose, for this example, you have the jbrowse programs in a separate 
directory that's a sibling of the genome1 and genome2 directories, so 
the whole thing looks like this:

genome1/
    data/
genome2/
    data/
jbrowse/
    bin/
       prepare-refseqs.pl
       flatfile-to-json.pl
       biodb-to-json.pl

When you set up, say, genome1, you need to run the JBrowse programs 
*from that directory*.  This is so that the relative paths used to write 
the files and the relative paths used in the URLs match up.  For 
example, something like this (in this case my config file is 
~/JBrowseConfig.js, and I'm only processing the reference sequence named 
"4"; those parts of the command line will probably vary in your case):

$ pwd
/var/www/html/genome1
$ ../jbrowse/bin/prepare-refseqs.pl --conf ~/JBrowseConfig.js --refs 4
$ ../jbrowse/bin/biodb-to-json.pl --conf ~/JBrowseConfig.js
$ ../jbrowse/bin/generate-names.pl

Then you have to create an html file for each genome.  Something like this:

$ cd ../jbrowse/
$ cp index.html genome1.html

Now edit genome1.html.  Find the lines referring to refSeqs.js and 
trackInfo.js:

<script type="text/javascript" src="data/refSeqs.js"></script>
<script type="text/javascript" src="data/trackInfo.js"></script>

and edit them to point to the genome1 directory, so that they look like 
this:

<script type="text/javascript" src="../genome1/data/refSeqs.js"></script>
<script type="text/javascript" src="../genome1/data/trackInfo.js"></script>

These can be either absolute or relative URLs.

Now, find the "Browser" constructor in the same genome1.html file:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback
                                });

and add the "dataRoot" parameter:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback,
                                    dataRoot: "../genome1/"
                                });

The "dataRoot" parameter has to refer to a directory on the same server 
that's serving the html page.  It can be either relative, with the ".." 
parent directory paths in the URL, or it can start with a / and be 
relative to the root on that server, like this:

                                    dataRoot: "/genome1/"

If you're generating the HTML with server-side code, you can do 
something analogous.

So, to summarize, you need to do three main things:

1. run the jbrowse programs from the "data" directory's parent directory
2. make it so that the html page loads refSeqs.js and trackInfo.js from 
the desired "data" directory
3. add the "dataRoot" parameter to the Browser constructor.

HTH,
Mitch

Re: [Gmod-ajax] Jbrowse Set Up Error

[Dave C. G. H. D. <he...@gm...>]

Hi Minh,

I'm CC'ing the JBrowse list as people there may have additional suggestions.

My guess is that JSON.pm was not installed on the system, or if it was
installed, it's in a place that is not in @INC.  A common cause of this is
installing JSON.pm as a regular user, rather than as root.

If you haven't already done so, please install JSON with CPAN.

Dave C.

On Thu, Jul 15, 2010 at 10:09 AM, <bui...@gm...> wrote:

> Hi,
> I am trying to set up Jbrowse on my Ubuntu Local Server.
> I follow this guide http://gmod.org/wiki/JBrowse_Tutorial. After I install
> everything, I run this command in my terminal:
> "bin/flatfile-to-json.pl" and get the following message.
>
> Can't locate JSON.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib
> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm
> line 10.
> BEGIN failed--compilation aborted at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 10.
> Compilation failed in require at /var/www/jbrowse/bin/flatfile-to-json.plline 13.
> BEGIN failed--compilation aborted at /var/www/jbrowse/bin/
> flatfile-to-json.pl line 13.
>
>
> Could you show me how to fix this???
>



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Re: [Gmod-ajax] A couple of questions (relative coordinates, multiple projects)

[Dave C. G. H. D. <he...@gm...>]

Hi David,

It looks like your GFF3 was answered (negatively) on the GBrowse list.

Did you resolve your second question yet, or is it still an open problem?

Thanks,

Dave C

On Sat, Jul 3, 2010 at 6:05 AM, David Breimann <dav...@gm...>wrote:

> Hello,
>
> 1. I'm trying to figure out how to use relative coordinates in a GFF
> file under JBrowse.
> Let's say I have I have a chromosome (chr1) of size 5Mbp. I loaded its
> sequence and annotations to JBrowse.
> Now I would like to focus on a specific region withing this chromosome
> (region1) of 100kb - let's say chr1:100001-200000, and use a GFF file
> (region1.gff) with coordinate relative to region1 (e.g. a feature in
> region.gff with coordinates 1 100 will be displayed on chr1
> 100001-100100).
> Is this possible?
>
> 2.I would like to have multiple JBrowse projects, each in a separate
> folder. I tried the --out options of the bin scripts bu then when I
> browsed to localhost/jbrowse I ended up with a blank age. Where should
> I point my browser?
>
> Thanks,
> David
>
>
> ------------------------------------------------------------------------------
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Re: [Gmod-ajax] Trouble behind cherrypy

[Ian H. <ih...@be...>]

It's hard to say; we're doing some refactoring now and it might "fall out" of that..
Sorry I cannot be more specific at this stage. Certainly what you ask for is a common request from people using jbrowse as part of a repository-type system, so I expect we would have this within the year, but don't hold me to it

Sent from my iPad

On Jul 12, 2010, at 12:57 AM, Mariette <jma...@to...> wrote:

> 
> Thanks for this answer.
> Do you think this fonctionnality will be coming up soon ?
> 
> Jerome
> 
> 
> 
> Ian Holmes a écrit :
>> Jerome, there is currently no way to do this but it is on our to-do
>> list. Ian
>> 
>> 
>> Mariette wrote:
>>  
>>> Hi everyone,
>>> I have a last question conserning jbrowse, I saw in the doc it is
>>> pssobile to provide to the jbrowse instance the seqRef.js and
>>> the trakInfo.js
>>> 
>>> *params*
>>>    a dictionary with the following keys:
>>> 
>>>        * |containerID| - ID of the HTML element that contains the browser
>>>        * |refSeqs| - list of reference sequence information items
>>>          (usually from refSeqs.js)
>>>        * |trackData| - list of track data items (usually from trackInfo.js)
>>>        * |dataRoot| - (optional) URL prefix for the data directory
>>>        * |browserRoot| - (optional) URL prefix for the browser code
>>>        * |tracks| - (optional) comma-delimited string containing
>>>          initial list of tracks to view
>>>        * |location| - (optional) string describing the initial location
>>>        * |defaultTracks| - (optional) comma-delimited string containing
>>>          initial list of tracks to view if there are no cookies and no
>>>          "tracks" parameter
>>>        * |defaultLocation| - (optional) string describing the initial
>>>          location if there are no cookies and no "location" parameter
>>> 
>>> However I'd like to give it whenever I want so jbrowse take in
>>> consideration different tracks/seqs files without reloading the
>>> page. How could that be done ??
>>> 
>>> I basicly want to do that because in our application users are allowed
>>> to delete/add/modify 'annotations' so I'd like to update the view
>>> when such actions are performed without reloading the web page (so
>>> .js files cannot be reloaded).
>>> 
>>> Thanks for your answer,
>>> Jerome
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Mariette a écrit :
>>>    
>>>> Hi Mitch,
>>>> 
>>>> so I'm getting further thanks for your help.
>>>> To explain you how we configure our site : we have multiple users, each with his own directory.
>>>> This directory is not seen by our web server (which is cherrypy). So far what we're doing is
>>>> to put the refSeq.js and the trackInfo.js in the user/project directory so this file is taken in
>>>> consideration when looking at the user quota (required for our site). To do so we basicly
>>>> have a dinamic link which return the right refSeq.js/trackInfo.js files considering the authentified
>>>> user.
>>>> 
>>>> Right now we have a problem with the link 'url' and 'seqDir' path as they have to be relative
>>>> to the web page where jbrowse is built.
>>>> How can we do to direct those links to our user directory ?? any idea ?
>>>> 
>>>> hope it make sense,
>>>> 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
>>>>        
>>> ------------------------------------------------------------------------------
>>> 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
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>>>    
>> 
>> ------------------------------------------------------------------------------
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>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>  

Re: [Gmod-ajax] Trouble behind cherrypy

[Mariette <jma...@to...>]

Thanks for this answer.
Do you think this fonctionnality will be coming up soon ?

Jerome



Ian Holmes a écrit :
> Jerome, there is currently no way to do this but it is on our to-do
> list. Ian
>
>
> Mariette wrote:
>   
>> Hi everyone,
>> I have a last question conserning jbrowse, I saw in the doc it is
>> pssobile to provide to the jbrowse instance the seqRef.js and
>> the trakInfo.js
>>
>> *params*
>>     a dictionary with the following keys:
>>
>>         * |containerID| - ID of the HTML element that contains the browser
>>         * |refSeqs| - list of reference sequence information items
>>           (usually from refSeqs.js)
>>         * |trackData| - list of track data items (usually from trackInfo.js)
>>         * |dataRoot| - (optional) URL prefix for the data directory
>>         * |browserRoot| - (optional) URL prefix for the browser code
>>         * |tracks| - (optional) comma-delimited string containing
>>           initial list of tracks to view
>>         * |location| - (optional) string describing the initial location
>>         * |defaultTracks| - (optional) comma-delimited string containing
>>           initial list of tracks to view if there are no cookies and no
>>           "tracks" parameter
>>         * |defaultLocation| - (optional) string describing the initial
>>           location if there are no cookies and no "location" parameter
>>
>> However I'd like to give it whenever I want so jbrowse take in
>> consideration different tracks/seqs files without reloading the
>> page. How could that be done ??
>>
>> I basicly want to do that because in our application users are allowed
>> to delete/add/modify 'annotations' so I'd like to update the view
>> when such actions are performed without reloading the web page (so
>> .js files cannot be reloaded).
>>
>> Thanks for your answer,
>> Jerome
>>
>>
>>
>>
>>
>>
>>
>> Mariette a écrit :
>>     
>>> Hi Mitch,
>>>
>>> so I'm getting further thanks for your help.
>>> To explain you how we configure our site : we have multiple users, each 
>>> with his own directory.
>>> This directory is not seen by our web server (which is cherrypy). So far 
>>> what we're doing is
>>> to put the refSeq.js and the trackInfo.js in the user/project directory 
>>> so this file is taken in
>>> consideration when looking at the user quota (required for our site). To 
>>> do so we basicly
>>> have a dinamic link which return the right refSeq.js/trackInfo.js files 
>>> considering the authentified
>>> user.
>>>
>>> Right now we have a problem with the link 'url' and 'seqDir' path as 
>>> they have to be relative
>>> to the web page where jbrowse is built.
>>> How can we do to direct those links to our user directory ?? any idea ?
>>>
>>> hope it make sense,
>>> 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
>>>   
>>>       
>> ------------------------------------------------------------------------------
>> 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
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>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>     
>
> ------------------------------------------------------------------------------
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>   

Re: [Gmod-ajax] Trouble behind cherrypy

[Ian H. <ih...@be...>]

Jerome, there is currently no way to do this but it is on our to-do
list. Ian


Mariette wrote:
> Hi everyone,
> I have a last question conserning jbrowse, I saw in the doc it is
> pssobile to provide to the jbrowse instance the seqRef.js and
> the trakInfo.js
> 
> *params*
>     a dictionary with the following keys:
> 
>         * |containerID| - ID of the HTML element that contains the browser
>         * |refSeqs| - list of reference sequence information items
>           (usually from refSeqs.js)
>         * |trackData| - list of track data items (usually from trackInfo.js)
>         * |dataRoot| - (optional) URL prefix for the data directory
>         * |browserRoot| - (optional) URL prefix for the browser code
>         * |tracks| - (optional) comma-delimited string containing
>           initial list of tracks to view
>         * |location| - (optional) string describing the initial location
>         * |defaultTracks| - (optional) comma-delimited string containing
>           initial list of tracks to view if there are no cookies and no
>           "tracks" parameter
>         * |defaultLocation| - (optional) string describing the initial
>           location if there are no cookies and no "location" parameter
> 
> However I'd like to give it whenever I want so jbrowse take in
> consideration different tracks/seqs files without reloading the
> page. How could that be done ??
> 
> I basicly want to do that because in our application users are allowed
> to delete/add/modify 'annotations' so I'd like to update the view
> when such actions are performed without reloading the web page (so
> .js files cannot be reloaded).
> 
> Thanks for your answer,
> Jerome
> 
> 
> 
> 
> 
> 
> 
> Mariette a écrit :
>> Hi Mitch,
>>
>> so I'm getting further thanks for your help.
>> To explain you how we configure our site : we have multiple users, each 
>> with his own directory.
>> This directory is not seen by our web server (which is cherrypy). So far 
>> what we're doing is
>> to put the refSeq.js and the trackInfo.js in the user/project directory 
>> so this file is taken in
>> consideration when looking at the user quota (required for our site). To 
>> do so we basicly
>> have a dinamic link which return the right refSeq.js/trackInfo.js files 
>> considering the authentified
>> user.
>>
>> Right now we have a problem with the link 'url' and 'seqDir' path as 
>> they have to be relative
>> to the web page where jbrowse is built.
>> How can we do to direct those links to our user directory ?? any idea ?
>>
>> hope it make sense,
>> 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
>>   
> 
> 
> ------------------------------------------------------------------------------
> 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

Re: [Gmod-ajax] Trouble behind cherrypy

[Mariette <jma...@to...>]

Hi everyone,
I have a last question conserning jbrowse, I saw in the doc it is
pssobile to provide to the jbrowse instance the seqRef.js and
the trakInfo.js

*params*
    a dictionary with the following keys:

        * |containerID| - ID of the HTML element that contains the browser
        * |refSeqs| - list of reference sequence information items
          (usually from refSeqs.js)
        * |trackData| - list of track data items (usually from trackInfo.js)
        * |dataRoot| - (optional) URL prefix for the data directory
        * |browserRoot| - (optional) URL prefix for the browser code
        * |tracks| - (optional) comma-delimited string containing
          initial list of tracks to view
        * |location| - (optional) string describing the initial location
        * |defaultTracks| - (optional) comma-delimited string containing
          initial list of tracks to view if there are no cookies and no
          "tracks" parameter
        * |defaultLocation| - (optional) string describing the initial
          location if there are no cookies and no "location" parameter

However I'd like to give it whenever I want so jbrowse take in
consideration different tracks/seqs files without reloading the
page. How could that be done ??

I basicly want to do that because in our application users are allowed
to delete/add/modify 'annotations' so I'd like to update the view
when such actions are performed without reloading the web page (so
.js files cannot be reloaded).

Thanks for your answer,
Jerome







Mariette a écrit :
> Hi Mitch,
>
> so I'm getting further thanks for your help.
> To explain you how we configure our site : we have multiple users, each 
> with his own directory.
> This directory is not seen by our web server (which is cherrypy). So far 
> what we're doing is
> to put the refSeq.js and the trackInfo.js in the user/project directory 
> so this file is taken in
> consideration when looking at the user quota (required for our site). To 
> do so we basicly
> have a dinamic link which return the right refSeq.js/trackInfo.js files 
> considering the authentified
> user.
>
> Right now we have a problem with the link 'url' and 'seqDir' path as 
> they have to be relative
> to the web page where jbrowse is built.
> How can we do to direct those links to our user directory ?? any idea ?
>
> hope it make sense,
> 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
>   

Re: [Gmod-ajax] Trouble behind cherrypy

[Mariette <jma...@to...>]

Hi Mitch,

so I'm getting further thanks for your help.
To explain you how we configure our site : we have multiple users, each 
with his own directory.
This directory is not seen by our web server (which is cherrypy). So far 
what we're doing is
to put the refSeq.js and the trackInfo.js in the user/project directory 
so this file is taken in
consideration when looking at the user quota (required for our site). To 
do so we basicly
have a dinamic link which return the right refSeq.js/trackInfo.js files 
considering the authentified
user.

Right now we have a problem with the link 'url' and 'seqDir' path as 
they have to be relative
to the web page where jbrowse is built.
How can we do to direct those links to our user directory ?? any idea ?

hope it make sense,
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
>>    
>

Re: [Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse

[sanjay s. <bea...@gm...>]

Hi Mitch,

Thanks,

Regards,
Sanjay



On Fri, Jul 2, 2010 at 6:47 PM, Mitch Skinner <mit...@be...>wrote:

>  Yes.  It's a bug, I'm aware of it, and I'm working on it, just like all
> the other bugs and shortcomings in JBrowse.  You've encountered the frontier
> of active JBrowse development, on the development branch.
>
> Mitch
>
>
> On 07/02/2010 12:01 AM, sanjay shah wrote:
>
> Hi Mitch,
>
> Thanks .But do that error really hampers the functionality of BAM files
> being visualized in Jbrowse(I mean is there any data ,information loss  due
> to this  in BAM to JSON conversion and visualization in Jbrowse.
>
>
>
> Thanks,
> Sanjay
>
> On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <mit...@be...>wrote:
>
>> 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.
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>
>
> --
> Success is how many times u smile each day every day.
>
>
>


-- 
Success is how many times u smile each day every day.

[Gmod-ajax] A couple of questions (relative coordinates, multiple projects)

[David B. <dav...@gm...>]

Hello,

1. I'm trying to figure out how to use relative coordinates in a GFF
file under JBrowse.
Let's say I have I have a chromosome (chr1) of size 5Mbp. I loaded its
sequence and annotations to JBrowse.
Now I would like to focus on a specific region withing this chromosome
(region1) of 100kb - let's say chr1:100001-200000, and use a GFF file
(region1.gff) with coordinate relative to region1 (e.g. a feature in
region.gff with coordinates 1 100 will be displayed on chr1
100001-100100).
Is this possible?

2.I would like to have multiple JBrowse projects, each in a separate
folder. I tried the --out options of the bin scripts bu then when I
browsed to localhost/jbrowse I ended up with a blank age. Where should
I point my browser?

Thanks,
David

Re: [Gmod-ajax] How can I display each feature name/tag/id/description next to it?

[David B. <dav...@gm...>]

Thanks a lot Mitch.

On Fri, Jul 2, 2010 at 7:26 PM, Mitch Skinner
<mit...@be...> wrote:
> On 07/02/2010 09:57 AM, David Breimann wrote:
>>
>> Thank you!
>>
>> 1. Is it possible to call a subroutine defined in extraData from label
>> (e.g. "label": "load_id")? I tried playing with the syntax, but
>> couldn't figure it out.
>>
>
> The "label" callback and the "extraData" callback both operate on bioperl
> feature objects.  So data doesn't go from the extraData outputs to the label
> callback, as you seem to be assuming.  Instead, in your "label" callback you
> get data straight from the source.  So, for example, you could so something
> like
>
> "label": "sub { return \"foo\" . $_[0]->attributes(\"load_id\"); }",
>
> to get whatever information you wanted, directly from the bioperl feature
> object.
>
>> 2. What is the structure of a feature object (read from a GFF)?
>>
>
> That's a bioperl thing; refer to the bioperl documentation.  When I want to
> experiment to learn a perl API, I often use Devel::REPL (installed from
> cpan), something like this:
>
> $ re.pl
>
> $ use Bio::DB::SeqFeature::Store
>
> $ my $db = Bio::DB::SeqFeature::Store->new(-dsn => "dbi:mysql:dmel_5_13")
> $Bio_DB_SeqFeature_Store_DBI_mysql1 =
> Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x97cae84);
>
> $ my @genes = $db->features(-seq_id => "4", -type => "gene")
>
> $ $genes[0]->attributes("load_id")
> FBgn0040037
>
>
> Mitch
>

Re: [Gmod-ajax] How can I display each feature name/tag/id/description next to it?

[Mitch S. <mit...@be...>]

On 07/02/2010 09:57 AM, David Breimann wrote:
> Thank you!
>
> 1. Is it possible to call a subroutine defined in extraData from label
> (e.g. "label": "load_id")? I tried playing with the syntax, but
> couldn't figure it out.
>    

The "label" callback and the "extraData" callback both operate on 
bioperl feature objects.  So data doesn't go from the extraData outputs 
to the label callback, as you seem to be assuming.  Instead, in your 
"label" callback you get data straight from the source.  So, for 
example, you could so something like

"label": "sub { return \"foo\" . $_[0]->attributes(\"load_id\"); }",

to get whatever information you wanted, directly from the bioperl 
feature object.

> 2. What is the structure of a feature object (read from a GFF)?
>    

That's a bioperl thing; refer to the bioperl documentation.  When I want 
to experiment to learn a perl API, I often use Devel::REPL (installed 
from cpan), something like this:

$ re.pl

$ use Bio::DB::SeqFeature::Store

$ my $db = Bio::DB::SeqFeature::Store->new(-dsn => "dbi:mysql:dmel_5_13")
$Bio_DB_SeqFeature_Store_DBI_mysql1 = 
Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x97cae84);

$ my @genes = $db->features(-seq_id => "4", -type => "gene")

$ $genes[0]->attributes("load_id")
FBgn0040037


Mitch

Re: [Gmod-ajax] How can I display each feature name/tag/id/description next to it?

[Mitch S. <mit...@be...>]

On 07/02/2010 07:28 AM, David Breimann wrote:
> I think it should be the default.
>
> Is it possible to do that using a config file?
> Also, I can I control the content of the label (e.g. define a sub that 
> uses the some fields in the last col of GFF to generate a nice looking 
> text, like done in GBrowse)?

For biodb-to-json.pl, it is the default; if you're not seeing labels 
then there may be something else going on.  By default, labels aren't 
shown until you're zoomed in beyond a certain point.  The threshold 
where labels are shown is configurable with the "clientConfig" setting 
in the config file.

You can define a sub to control the content of the label with the 
"label" setting in the config file.

Here's an example config file track setup showing both of those things:

     {
       "track": "gene",
       "key": "Gene Span",
       "feature": ["gene"],
       "autocomplete": "all",
       "class": "feature2",
       "category": "Gene Model features",
       "urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
       "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"},
       "label": "sub { return \"foo\" . $_[0]->display_name; }",
       "clientConfig": {
         "labelScale": 2
       }
     },

For the "label" setting, the value should be a string containing a perl 
callback; the first argument to the sub will be the feature object.  The 
callback should return the label that you want.

For the "clientConfig" entry, the "labelScale" setting controls the 
threshold where labels are shown; higher numbers make the threshold more 
zoomed-in, lower numbers make the threshold more zoomed-out.

The actual units for the "labelScale" setting are pixels/feature.  That 
value is multiplied by the average feature density (i.e., the number of 
features in the track / the refseq length) to get the scale threshold in 
pixels per base.  For example, if the labelScale is 2, and a track has 
100 features, then labels will be shown if you're zoomed in far enough 
that the entire refseq would be at least 200 pixels wide.

Practically speaking, the default labelScale is 50, and if you want the 
threshold to be more zoomed out, set labelScale lower until you see 
labels at the zoom level you want.

Mitch

Re: [Gmod-ajax] Graphs

[David B. <dav...@gm...>]

>
> Hi Ian and thanks for the quick reply.
>
> As for #1, thanks for the suggestion. I will look into BigWig.
> As for #2, I would love to get more info about the ImageTrack module.
>
> Let tell you a little bit about how I came to use JBrowse.
> I joined a lab where a couple of standalone (off-line) genome browsers were
> used for a long time. I felt they are really limited so I started looking
> for alternatives.
> GBrowse came up as a leading option, but was a bit disappointed with its
> performance. We use to scroll whole-genomes start to end, so speedy
> scrolling is a must. This was actually almost the single flaw of GBrowse for
> me. If I could only browse faster ("continuously") - it would be great
> (maybe I am missing some trick here?)
>
> I should admit it took me some time to find about JBrowse, but the online
> demonstration was really cool and fast. I am now experiencing with it. My
> first impression is very good, but I feel there are many things missing.
> Some of them are:
> - better interaction: be able to zoom in on selection, export selected
> sequence, use keyboard shortcuts
> - better graphing capabilities (as mentioned in my original post): muktiple
> graphs in the same track, show value when cursor is on graph, show scale
>
> Anyway, I hope you continue the great work and make this great tool even
> better.
>
> Best,
> David
>
>
> On Fri, Jul 2, 2010 at 6:05 PM, Ian Holmes <ih...@be...> wrote:
>
>> Hi David,
>>
>> For #1 do you mean the wig file takes a long time to process, or the
>> resulting image file takes a ling time to load? If the former, yes there is
>> a binary format (BigWig) that could be explored.
>>
>> For #2, the jbrowse client can display any (appropriately processed)
>> image, so it's possible in theory. Our strategy is to develop general
>> software components so that you can write programs on the server yourself to
>> do this. There is, for example, a Perl module that allows you to draw
>> arbitrary graphics primitives onto jbrowse tracks. The particular use case
>> you mentioned (multiple variates on the same plot, using color) is quite a
>> common request and will probably be bundled with jbrowse eventually, but not
>> yet. In the meantime if you are interested in the roll-your-own approach,
>> check out the ImageTrack perl module in the jbrowse source tree. I can send
>> you more info on this if you like.
>>
>> #3 is definitely on our to-do list, near the top.
>>
>> Best wishes
>> Ian
>>
>> On Jul 2, 2010, at 7:51 AM, David Breimann <dav...@gm...>
>> wrote:
>>
>> Hello,
>>
>> I have calculate different scores for each nucleotide in the genome (each
>> score is just a list of numbers which length is the length of the genome). I
>> added a wig header to each score file (fixed step, start = 1, step = 1), and
>> I successfully added such graphs to my JBrowse using
>> <http://wig-to-json.pl>wig-to-json.pl.
>> I have a few questions:
>>
>> 1. Loading these wig file take a long of time. I understand this are heavy
>> graphs, but perhaps there's a better way to present such data other than
>> wig? I guess not, but wonder anyhow.
>>
>> 2. I would like to display a couple of graphs on the same track (different
>> colors). How can this be done? Preferably, the graphs should not be filled
>> (just line plots).
>>
>> 3. I would like to display an axis (ruler) at the edge of the view to get
>> an idea about the values.
>>
>> Is this possible in JBrowse?
>>
>> Thanks,
>> David
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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>
>> http://p.sf.net/sfu/sprint-com-first
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>

Re: [Gmod-ajax] Graphs

[Ian H. <ih...@be...>]

Hi David,

For #1 do you mean the wig file takes a long time to process, or the resulting image file takes a ling time to load? If the former, yes there is a binary format (BigWig) that could be explored.

For #2, the jbrowse client can display any (appropriately processed) image, so it's possible in theory. Our strategy is to develop general software components so that you can write programs on the server yourself to do this. There is, for example, a Perl module that allows you to draw arbitrary graphics primitives onto jbrowse tracks. The particular use case you mentioned (multiple variates on the same plot, using color) is quite a common request and will probably be bundled with jbrowse eventually, but not yet. In the meantime if you are interested in the roll-your-own approach, check out the ImageTrack perl module in the jbrowse source tree. I can send you more info on this if you like.

#3 is definitely on our to-do list, near the top.

Best wishes
Ian 

On Jul 2, 2010, at 7:51 AM, David Breimann <dav...@gm...> wrote:

> Hello,
> 
> I have calculate different scores for each nucleotide in the genome (each score is just a list of numbers which length is the length of the genome). I added a wig header to each score file (fixed step, start = 1, step = 1), and I successfully added such graphs to my JBrowse using wig-to-json.pl.
> I have a few questions:
> 
> 1. Loading these wig file take a long of time. I understand this are heavy graphs, but perhaps there's a better way to present such data other than wig? I guess not, but wonder anyhow.
> 
> 2. I would like to display a couple of graphs on the same track (different colors). How can this be done? Preferably, the graphs should not be filled (just line plots).
> 
> 3. I would like to display an axis (ruler) at the edge of the view to get an idea about the values.
> 
> Is this possible in JBrowse?
> 
> Thanks,
> David
> 
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] Graphs

[David B. <dav...@gm...>]

Hello,

I have calculate different scores for each nucleotide in the genome (each
score is just a list of numbers which length is the length of the genome). I
added a wig header to each score file (fixed step, start = 1, step = 1), and
I successfully added such graphs to my JBrowse using wig-to-json.pl.
I have a few questions:

1. Loading these wig file take a long of time. I understand this are heavy
graphs, but perhaps there's a better way to present such data other than
wig? I guess not, but wonder anyhow.

2. I would like to display a couple of graphs on the same track (different
colors). How can this be done? Preferably, the graphs should not be filled
(just line plots).

3. I would like to display an axis (ruler) at the edge of the view to get an
idea about the values.

Is this possible in JBrowse?

Thanks,
David

Re: [Gmod-ajax] How can I display each feature name/tag/id/description next to it?

[Mitch S. <mit...@be...>]

With flatfile-to-json.pl, add the --getLabels command line argument.  
I'm starting to think that should be the default.

Mitch

On 07/02/2010 06:50 AM, David Breimann wrote:
> Currently, all my features show only the glyph, with no 
> name/description next (or no) them.
> How can I control this?
>
> Thanks,
> David
>
>
> ------------------------------------------------------------------------------
> 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
>    

[Gmod-ajax] How can I display each feature name/tag/id/description next to it?

[David B. <dav...@gm...>]

Currently, all my features show only the glyph, with no name/description
next (or no) them.
How can I control this?

Thanks,
David

Re: [Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse

[Mitch S. <mit...@be...>]

Yes.  It's a bug, I'm aware of it, and I'm working on it, just like all 
the other bugs and shortcomings in JBrowse.  You've encountered the 
frontier of active JBrowse development, on the development branch.

Mitch

On 07/02/2010 12:01 AM, sanjay shah wrote:
> Hi Mitch,
>
> Thanks .But do that error really hampers the functionality of BAM 
> files being visualized in Jbrowse(I mean is there any data 
> ,information loss  due to this  in BAM to JSON conversion and 
> visualization in Jbrowse.
>
>
>
> Thanks,
> Sanjay
>
> On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner 
> <mit...@be... <mailto:mit...@be...>> wrote:
>
>     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 :
>          $$ bin/flatfile-to-json.pl <http://flatfile-to-json.pl>  --bam
>           /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam
>         --cssclass exon
>           --tracklabel BAM_data --key "BAM Data"
>
>
>          which   throws the  following error
>
>         Use of uninitialized value in int at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>         Use of uninitialized value in subtraction (-) at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>         Use of uninitialized value in int at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>         Use of uninitialized value in subtraction (-) at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>         Use of uninitialized value in int at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>         Use of uninitialized value in subtraction (-) at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>         Use of uninitialized value in int at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>         Use of uninitialized value in subtraction (-) at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>         Use of uninitialized value in int at
>         /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>
>
>         please help ..Thanks
>
>         Thanks,
>         Sanjay
>
>
>
>
>         Thanks,
>         Sanjay
>
>         On Wed, Jun 23, 2010 at 2:10 PM, sanjay
>         shah<bea...@gm... <mailto:bea...@gm...>>  wrote:
>
>             Hi ,
>
>             Thanks.I  did sort  the alignments and  then  created
>             index manually
>             with samtools( I  have "20100311.sorted.bam.bai " file ) ;
>             now when I
>             again try to convert BAM to JSON by issuing command as:
>
>
>              $$ bin/flatfile-to-json.pl <http://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...
>             <mailto: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
>                     <http://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.

Re: [Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse

[sanjay s. <bea...@gm...>]

Hi Mitch,

Thanks .But do that error really hampers the functionality of BAM files
being visualized in Jbrowse(I mean is there any data ,information loss  due
to this  in BAM to JSON conversion and visualization in Jbrowse.



Thanks,
Sanjay

On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <mit...@be...>wrote:

> 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.
>>>
>>>
>>>
>>
>>
>>
>>
>
>


-- 
Success is how many times u smile each day every day.

Re: [Gmod-ajax] jbrowse display:none

[Mitch S. <mit...@be...>]

Hmmm, I hadn't thought about this kind of usage.

When JBrowse starts up, it puts some UI elements on the screen, and it 
measures how big those are (because some of the layout JBrowse does 
can't be done, as far as I know, in pure CSS; the JBrowse javascript 
calculates the positions/sizes of some of the JBrowse UI elements 
itself).  But if those UI elements aren't displayed, then I would 
imagine that the results of the size measurements would be wrong, or 
undefined, or somehow not what JBrowse expects.

I'm speculating; it would be easier to diagnose if you could send me a 
URL so that I could see what's going on myself.  But, assuming that I'm 
guessing correctly about what the problem is, then I think the solution 
is to run the Browser constructor only after the "GenomeBrowser" element 
has been displayed.

Specifically, somewhere in the page you presumably currently have 
something like this:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback
                                });

What you can do is remove that "new Browser" call from its current 
location on the page, and put in into the onclick handler instead, after 
you set style.display='block'.

I'm not sure what would happen if the JBrowse element is displayed, then 
hidden, then displayed again; you might have to remove the element from 
the page entirely and then recreate it when you want it to be shown 
again.  In other words, bad things will probably happen if you run the 
Browser constructor more than once with the same element as the 
container, but you should be safe if you remove and recreate that 
element before you run the Browser constructor again.

Hope this helps,
Mitch

On 07/01/2010 07:44 AM, Philippe Bardou wrote:
> 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
>>
>
> ------------------------------------------------------------------------------
> 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
>    

Re: [Gmod-ajax] using multiple sources

[Mitch S. <mit...@be...>]

Hi, sorry it took so long to get back to you; I had a big deadline that 
I had to focus on for a while instead.

I spent some time looking at this; I was thinking of changing the 
behavior of the dataRoot setting.  But I realized that that would 
require people to re-generate their JBrowse JSON.  So don't think we 
want to do that in the current "master" branch, although it might make 
sense to do it in the current development ("lazyfeatures") branch.

So, assuming you're using the master branch, then there's one more 
option that I forgot to mention in my last email, that should make the 
name searching work, without requiring you to have multiple copies of 
the JBrowse code.  It's a bit awkward, though.

Earlier, I suggested that you have multiple data directories, with 
separate html files that pointed to them, something like this:

jbrowse/
    genome1-data/
    genome2-data/
    genome1.html
    genome2.html

The awkward thing that I forgot to suggest earlier is this: take those 
genome1-data and genome2-data directories, and rename them and move them 
around so that they look like this instead:

jbrowse/
    genome1.html
    genome2.html

genome1/
    data/

genome2/
    data/

That is, take those data directories and make them into directories 
named "data", with uniquely named parent directories.  This is because 
that "data" string (unfortunately) shows up in several places both in 
the JBrowse code and also in the generated JSON.

Then update genome1.html and genome2.html so that the refSeqs.js and 
trackInfo.js links point to where you moved those data directories; e.g.:

<script type="text/javascript" src="../genome1/data/refSeqs.js"></script>
<script type="text/javascript" src="../genome1/data/trackInfo.js"></script>


And then add the "dataRoot" option to the Browser constructor in 
genome1.html and genome2.html, so that it looks something like this:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback,
                                    dataRoot: "../genome1"
                                });


and that ought to do it.  I haven't tested the specific recommendations 
in this email, though, so do let me know if it works for you.

Mitch


On 06/01/2010 08:17 AM, Adam Witney wrote:
> On 28 May 2010, at 19:13, Mitch Skinner wrote:
>    
>> So, right now you've got two options:
>>
>> 1. have separate JBrowse directories will both code and data, or
>> 2. wait a few days or a week for us to fix up the dataRoot setting to be more flexible.
>>
>> If you choose option 1, and if you originally got JBrowse using git, then you can save some disk space by using "git clone".  For example, if you originally did a "git clone" to create a "jbrowse" directory, you can clone from there to a new directory, and the clone will save some disk space (by using hard-linking).
>>
>> $ git clone jbrowse genome1
>> $ git clone jbrowse genome2
>>
>> will give you new "genome1" and "genome2" directories that don't use much extra disk space.
>>
>> Sorry about that,
>> Mitch
>>      
> ok thanks for the tips Mitch, I will try those options
>
> thanks
>
> adam
>
>
>