[Gmod-ajax] Regarding JBrowse

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[Gmod-ajax] Regarding JBrowse

Vijay Bhasker
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: Regarding JBrowse

nathandunn

This is a good starting point:



Nathan

On Aug 15, 2016, at 6:58 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: Regarding JBrowse

Scott Cain
In reply to this post by Vijay Bhasker
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: Regarding JBrowse

Vijay Bhasker


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;scott@scottcain.net&#39;);" target="_blank">scott@...> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
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Re: Regarding JBrowse

Scott Cain
Hi Vijay,

Hopefully you are using a browser like Chrome where you can open View->Developer->Javascript console and then reload the JBrowse page (opening the JS console forces all of the page to reload, rather than using the cache--I think that's on by default).  Also, when you're asking about commands you performed, it is a good idea to actually copy the command into the email, so we can see it and give pointers or better tune our responses.

Scott


On Mon, Aug 15, 2016 at 3:26 PM, Vijay Bhasker <[hidden email]> wrote:


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
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Re: Regarding JBrowse

Vijay Bhasker
Hi GMOD

I have run the flatfile-to-json.pl file without any error. And I would like to know how to see the changes applied by this command.Also what should I do with the "Feature tracks" module i.e; where to use those options. So, can anyone please tell me what to do after running the flatfile-to-json.pl command.

Thanks.

Regards
Vijay.

On Mon, Aug 15, 2016 at 3:37 PM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Hopefully you are using a browser like Chrome where you can open View->Developer->Javascript console and then reload the JBrowse page (opening the JS console forces all of the page to reload, rather than using the cache--I think that's on by default).  Also, when you're asking about commands you performed, it is a good idea to actually copy the command into the email, so we can see it and give pointers or better tune our responses.

Scott


On Mon, Aug 15, 2016 at 3:26 PM, Vijay Bhasker <[hidden email]> wrote:


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------

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Re: Regarding JBrowse

Scott Cain
Hi  Vijay,

Again, it's a good idea to include the complete command you used when asking for help, since you might have done something we didn't expect, or left something out that is needed.  Also, telling us the URL you're using would help too (even if it's an internal URL that we can't get to).

That said, you should be able to just refresh your browser where you expect JBrowse to be, with caching turned off so it will reload the config files.

Scott


On Tue, Aug 16, 2016 at 11:42 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I have run the flatfile-to-json.pl file without any error. And I would like to know how to see the changes applied by this command.Also what should I do with the "Feature tracks" module i.e; where to use those options. So, can anyone please tell me what to do after running the flatfile-to-json.pl command.

Thanks.

Regards
Vijay.

On Mon, Aug 15, 2016 at 3:37 PM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Hopefully you are using a browser like Chrome where you can open View->Developer->Javascript console and then reload the JBrowse page (opening the JS console forces all of the page to reload, rather than using the cache--I think that's on by default).  Also, when you're asking about commands you performed, it is a good idea to actually copy the command into the email, so we can see it and give pointers or better tune our responses.

Scott


On Mon, Aug 15, 2016 at 3:26 PM, Vijay Bhasker <[hidden email]> wrote:


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------

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Re: Regarding JBrowse

Vijay Bhasker
Hi

From the start after ./setup.sh, I ran bin/prepare-refseqs.pl --fasta <path to volvox.fa> and bin/prepare-refseqs.pl --gff <path to volvox.gff3>. Later I ran bin/flatfile-to-json.pl --gff volvox.gff3 --tracklabel <track name> with no errors. That's all. I am looking into feature tracks but not getting to know where to use them.

Thanks.

Regards
Vijay.

On Tue, Aug 16, 2016 at 4:30 PM, Scott Cain <[hidden email]> wrote:
Hi  Vijay,

Again, it's a good idea to include the complete command you used when asking for help, since you might have done something we didn't expect, or left something out that is needed.  Also, telling us the URL you're using would help too (even if it's an internal URL that we can't get to).

That said, you should be able to just refresh your browser where you expect JBrowse to be, with caching turned off so it will reload the config files.

Scott


On Tue, Aug 16, 2016 at 11:42 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I have run the flatfile-to-json.pl file without any error. And I would like to know how to see the changes applied by this command.Also what should I do with the "Feature tracks" module i.e; where to use those options. So, can anyone please tell me what to do after running the flatfile-to-json.pl command.

Thanks.

Regards
Vijay.

On Mon, Aug 15, 2016 at 3:37 PM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Hopefully you are using a browser like Chrome where you can open View->Developer->Javascript console and then reload the JBrowse page (opening the JS console forces all of the page to reload, rather than using the cache--I think that's on by default).  Also, when you're asking about commands you performed, it is a good idea to actually copy the command into the email, so we can see it and give pointers or better tune our responses.

Scott


On Mon, Aug 15, 2016 at 3:26 PM, Vijay Bhasker <[hidden email]> wrote:


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------

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Re: Regarding JBrowse

Scott Cain
Hi Vijay,

What URL did you use to see the sample data?  Was it something like


If so, you should probably just be able to strip the stuff off starting at the question mark, and go to this url:


(or similarly with what ever host/URL you're using).

Scott


On Tue, Aug 16, 2016 at 10:57 PM, Vijay Bhasker <[hidden email]> wrote:
Hi

From the start after ./setup.sh, I ran bin/prepare-refseqs.pl --fasta <path to volvox.fa> and bin/prepare-refseqs.pl --gff <path to volvox.gff3>. Later I ran bin/flatfile-to-json.pl --gff volvox.gff3 --tracklabel <track name> with no errors. That's all. I am looking into feature tracks but not getting to know where to use them.

Thanks.

Regards
Vijay.

On Tue, Aug 16, 2016 at 4:30 PM, Scott Cain <[hidden email]> wrote:
Hi  Vijay,

Again, it's a good idea to include the complete command you used when asking for help, since you might have done something we didn't expect, or left something out that is needed.  Also, telling us the URL you're using would help too (even if it's an internal URL that we can't get to).

That said, you should be able to just refresh your browser where you expect JBrowse to be, with caching turned off so it will reload the config files.

Scott


On Tue, Aug 16, 2016 at 11:42 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I have run the flatfile-to-json.pl file without any error. And I would like to know how to see the changes applied by this command.Also what should I do with the "Feature tracks" module i.e; where to use those options. So, can anyone please tell me what to do after running the flatfile-to-json.pl command.

Thanks.

Regards
Vijay.

On Mon, Aug 15, 2016 at 3:37 PM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Hopefully you are using a browser like Chrome where you can open View->Developer->Javascript console and then reload the JBrowse page (opening the JS console forces all of the page to reload, rather than using the cache--I think that's on by default).  Also, when you're asking about commands you performed, it is a good idea to actually copy the command into the email, so we can see it and give pointers or better tune our responses.

Scott


On Mon, Aug 15, 2016 at 3:26 PM, Vijay Bhasker <[hidden email]> wrote:


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
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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

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Re: Regarding JBrowse

Vijay Bhasker
Hi Scott

I tried using http:// localhost/jbrowse/JBrowse-1.11.0/index.html as mentioned in the tutorial. So, I went into the file system /var/www/jbrowse/JBrowse-1.11.0/index.html? and opened it in the browser.Also I have a doubt of how to use these HTMLFeature Configuration Options.

Regards
Vijay.

On Wed, Aug 17, 2016 at 11:16 AM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

What URL did you use to see the sample data?  Was it something like


If so, you should probably just be able to strip the stuff off starting at the question mark, and go to this url:


(or similarly with what ever host/URL you're using).

Scott


On Tue, Aug 16, 2016 at 10:57 PM, Vijay Bhasker <[hidden email]> wrote:
Hi

From the start after ./setup.sh, I ran bin/prepare-refseqs.pl --fasta <path to volvox.fa> and bin/prepare-refseqs.pl --gff <path to volvox.gff3>. Later I ran bin/flatfile-to-json.pl --gff volvox.gff3 --tracklabel <track name> with no errors. That's all. I am looking into feature tracks but not getting to know where to use them.

Thanks.

Regards
Vijay.

On Tue, Aug 16, 2016 at 4:30 PM, Scott Cain <[hidden email]> wrote:
Hi  Vijay,

Again, it's a good idea to include the complete command you used when asking for help, since you might have done something we didn't expect, or left something out that is needed.  Also, telling us the URL you're using would help too (even if it's an internal URL that we can't get to).

That said, you should be able to just refresh your browser where you expect JBrowse to be, with caching turned off so it will reload the config files.

Scott


On Tue, Aug 16, 2016 at 11:42 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I have run the flatfile-to-json.pl file without any error. And I would like to know how to see the changes applied by this command.Also what should I do with the "Feature tracks" module i.e; where to use those options. So, can anyone please tell me what to do after running the flatfile-to-json.pl command.

Thanks.

Regards
Vijay.

On Mon, Aug 15, 2016 at 3:37 PM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Hopefully you are using a browser like Chrome where you can open View->Developer->Javascript console and then reload the JBrowse page (opening the JS console forces all of the page to reload, rather than using the cache--I think that's on by default).  Also, when you're asking about commands you performed, it is a good idea to actually copy the command into the email, so we can see it and give pointers or better tune our responses.

Scott


On Mon, Aug 15, 2016 at 3:26 PM, Vijay Bhasker <[hidden email]> wrote:


On Monday, August 15, 2016, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD 

I have done the prepare-refseqs.pl with fasta and gff and also done flatfile-to-json.pl with gff file volvox.gff3 with track label "dna" and where should I look for these changes to display i.e; how to see the commands executed so far .

Thanks
Vijay.

On Monday, August 15, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

The categories on the left don't "mean" anything; they are useful labels that you (the administrator who sets of JBrowse) can add to groups of tracks that logically (to you) belong together.  I wouldn't worry about them first; rather, I'd suggest looking into how prepare-refseqs.pl and flatfile-to-json.pl work, as they are the tools you will need to do the fundamental stuff of getting things to display in JBrowse.

Scott
 

On Mon, Aug 15, 2016 at 9:58 AM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

I would like to know what exactly the categories of features in the left side of the window mean. Also I would like to know how to add features to Jbrowse with some new configurations. Hope some tutorials on Jbrowse can help.

Thanks in advance.

Regards
Vijay.

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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