[Gmod-ajax] Not able to call jbrowse in browser

[ajay kumar]

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

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[Eric Yao]

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

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[ajay kumar]

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

--

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[Eric Yao]

Hi Ajay,

A good place to start is here:

http://jbrowse.org/code/JBrowse-1.12.1/docs/tutorial/

The example shows how to import your gff file among other.

On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

--

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[ajay kumar]

Respected Sir,

I have finished the tutorial.

And now able to run jbrowse with my own data set..

But I could not understand how I can change viewing pattern of the track also color of track. Like white  to red. Or blue

Please help me as I am very much new to this domain.

Waitimg.for your kind response.

Thanks and Warm Regards

Ajay

On Apr 11, 2017 1:18 AM, "Eric Yao" <[hidden email]> wrote:

Hi Ajay,

A good place to start is here:

http://jbrowse.org/code/JBrowse-1.12.1/docs/tutorial/

The example shows how to import your gff file among other.

On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

--

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[Eric Yao]

Hi Ajay,

This is the detailed reference for configuration options for your tracks (in trackList.json):

http://gmod.org/wiki/JBrowse_Configuration_Guide#Feature_Tracks_.28HTMLFeatures_and_CanvasFeatures.29

This configuration in your track config determines whether you are using either CanvasFeatures viewer or HTMLFeatures viewer.

"type": "JBrowse/View/Track/HTMLFeatures",

On Mon, Apr 10, 2017 at 12:54 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I have finished the tutorial.

And now able to run jbrowse with my own data set..

But I could not understand how I can change viewing pattern of the track also color of track. Like white  to red. Or blue

Please help me as I am very much new to this domain.

Waitimg.for your kind response.

Thanks and Warm Regards

Ajay

On Apr 11, 2017 1:18 AM, "Eric Yao" <[hidden email]> wrote:

Hi Ajay,

A good place to start is here:

http://jbrowse.org/code/JBrowse-1.12.1/docs/tutorial/

The example shows how to import your gff file among other.

On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

--

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[Scott Cain]

Hi Ajay,

There is also this tutorial that I sometimes give:

http://gmod.org/wiki/JBrowse_Tutorial_PAG_2017#Changing_the_way_tracks_look

It tries to go into a little more depth on some topics, like changing how the track looks.

Scott

On Mon, Apr 10, 2017 at 4:08 PM, Eric Yao <[hidden email]> wrote:

Hi Ajay,

This is the detailed reference for configuration options for your tracks (in trackList.json):

http://gmod.org/wiki/JBrowse_Configuration_Guide#Feature_Tracks_.28HTMLFeatures_and_CanvasFeatures.29

This configuration in your track config determines whether you are using either CanvasFeatures viewer or HTMLFeatures viewer.

"type": "JBrowse/View/Track/HTMLFeatures",

On Mon, Apr 10, 2017 at 12:54 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I have finished the tutorial.

And now able to run jbrowse with my own data set..

But I could not understand how I can change viewing pattern of the track also color of track. Like white  to red. Or blue

Please help me as I am very much new to this domain.

Waitimg.for your kind response.

Thanks and Warm Regards

Ajay

On Apr 11, 2017 1:18 AM, "Eric Yao" <[hidden email]> wrote:

Hi Ajay,

A good place to start is here:

http://jbrowse.org/code/JBrowse-1.12.1/docs/tutorial/

The example shows how to import your gff file among other.

On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

--

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[Eric Yao]

oh, very nice, scott!

On Mon, Apr 10, 2017 at 2:27 PM, Scott Cain <[hidden email]> wrote:

Hi Ajay,

There is also this tutorial that I sometimes give:

http://gmod.org/wiki/JBrowse_Tutorial_PAG_2017#Changing_the_way_tracks_look

It tries to go into a little more depth on some topics, like changing how the track looks.

Scott

On Mon, Apr 10, 2017 at 4:08 PM, Eric Yao <[hidden email]> wrote:

Hi Ajay,

This is the detailed reference for configuration options for your tracks (in trackList.json):

http://gmod.org/wiki/JBrowse_Configuration_Guide#Feature_Tracks_.28HTMLFeatures_and_CanvasFeatures.29

This configuration in your track config determines whether you are using either CanvasFeatures viewer or HTMLFeatures viewer.

"type": "JBrowse/View/Track/HTMLFeatures",

On Mon, Apr 10, 2017 at 12:54 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I have finished the tutorial.

And now able to run jbrowse with my own data set..

But I could not understand how I can change viewing pattern of the track also color of track. Like white  to red. Or blue

Please help me as I am very much new to this domain.

Waitimg.for your kind response.

Thanks and Warm Regards

Ajay

On Apr 11, 2017 1:18 AM, "Eric Yao" <[hidden email]> wrote:

Hi Ajay,

A good place to start is here:

http://jbrowse.org/code/JBrowse-1.12.1/docs/tutorial/

The example shows how to import your gff file among other.

On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:

Respected Sir,

Thanks for your prompt reply, and suggestion

I have solve the issue i have configured  apache2 webserver and now i can able to run the locally configured jbrowse in browser.

I will try the desktop version.

Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?.

Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you

Once again Thank you

Warm Regards

Ajay

On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:

Have you setup a webserver and configured it to point to the directory where you've installed jbrowse?

There are also desktop versions you can try:

http://jbrowse.org/jbrowse-1-12-1/

On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:

Respected Sir,

I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt

**************************

ajay@ajay-Precision-Tower-7910[akm] ./setup.sh                        [ 6:25PM]

Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

ajay@ajay-Precision-Tower-7910[akm]   ****

*******************************

Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like 

opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working.

Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience.

Waiting for your reply and suggestion to solve this problem.

Thanks and Warm Regards

--

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