[Gmod-ajax] Add a Header and Footer option ?

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[Gmod-ajax] Add a Header and Footer option ?

FredBGA

Hello

 

We were using GBrowse a lot. We set up now JBrowse instead.

And there are some useful and convenient functionalities that are missing within JBrowse.

 

Is there a way to add easily a Footer and Header just like in GBrowse configuration file ?

Right now it’s not so easy for a user to guess which genome is currently displayed.

aboutThisBrowser→description is not enough, you have to click in order to get the information.

 

ie : if I want to browse the JBrowse set up by Scott in his last message to the list ( http://agrjbrowsestatic.s3-website-us-east-1.amazonaws.com/) how can I guess the genome used as reference ? There is no Citation for the reference track. The only way is maybe to look the URL, or try to guess using the prefix in chromosomes names or blast a piece of the sequence J

 

To date I have used the dataset selector but again it’s not as clear and simple as a Header.

 

Thank you.

 

Fred

 

---

Frederic Sapet

Bioinformatics Research Engineer

BIOGEMMA - Upstream Genomics Group

Centre de Recherche de Chappes

CS 90126

63720 CHAPPES

FRANCE

Tel : +33 (0)4 73 67 88 54

Fax : +33 (0)4 73 67 88 99

E-mail : [hidden email]

 


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Re: Add a Header and Footer option ?

Scott Cain
Hi Fred,

I didn't turn on the "classic menu" in the S3 JBrowse because I wanted to touch the config as little as possible while I was debugging, but I agree, having that on is more of a bare minimum.  At WormBase, we have a header and footer on JBrowse:


Since the JBrowse page is a "simple" html index file, we just edited it until it looked more or less the way we wanted it (I toyed with the idea of making the index file an index.shtml file and doing the header and footer via includes but decided it wasn't worth the effort).  Now, I can say that I don't particularly like the result--particularly the footer.  To make the footer appear, I had to make the div that JBrowse appeared in have a fixed height, which means that some times, users have to scroll inside the JBrowse div to see content.  Since I don't like that for a user interface, I also provide a button ("Full page") that lets users switch to a JBrowse view without any of the header or footers.  If I didn't have a mandate to include the footer, I would have just gone with a header.

Anyway, all of this is to say that there is a fundamental difference between GBrowse and JBrowse in this regard: in GBrowse, you really need the header and footer options in the config, since the cgi is creating the page and there is no other way to inject content into the page other than via the cgi code.  With JBrowse, since the code is in an html page, you can just edit it to look the way you want, so I don't think it's necessary to have those options in the config.

Scott


On Fri, Apr 28, 2017 at 3:32 AM, SAPET, Frederic <[hidden email]> wrote:

Hello

 

We were using GBrowse a lot. We set up now JBrowse instead.

And there are some useful and convenient functionalities that are missing within JBrowse.

 

Is there a way to add easily a Footer and Header just like in GBrowse configuration file ?

Right now it’s not so easy for a user to guess which genome is currently displayed.

aboutThisBrowser→description is not enough, you have to click in order to get the information.

 

ie : if I want to browse the JBrowse set up by Scott in his last message to the list ( http://agrjbrowsestatic.s3-website-us-east-1.amazonaws.com/) how can I guess the genome used as reference ? There is no Citation for the reference track. The only way is maybe to look the URL, or try to guess using the prefix in chromosomes names or blast a piece of the sequence J

 

To date I have used the dataset selector but again it’s not as clear and simple as a Header.

 

Thank you.

 

Fred

 

---

Frederic Sapet

Bioinformatics Research Engineer

BIOGEMMA - Upstream Genomics Group

Centre de Recherche de Chappes

CS 90126

63720 CHAPPES

FRANCE

Tel : <a href="tel:+33%204%2073%2067%2088%2054" value="+33473678854" target="_blank">+33 (0)4 73 67 88 54

Fax : <a href="tel:+33%204%2073%2067%2088%2099" value="+33473678899" target="_blank">+33 (0)4 73 67 88 99

E-mail : [hidden email]

 


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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: Add a Header and Footer option ?

FredBGA

Hi Scott

 

sorry I didn't mean that your browser was poorly configured, I use it as example because it's freely accessible. my own browsers cannot be accessed publicly (and are basically configured)

 

For my purpose, modifying the index.html is not my favorite solution.

I prefer a solution related to the trackList file. indeed I would like to have an unique header for each genome (maybe something like that, with a karyotype - http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). The index.html will give me one header for all of them, right ?

by the way, the dataset selector could be enough. But how can I display the name of the current genome ?  Right now, it shows "Genome". When I click I see "Open sequence file" and the list of my configured genomes.

 

Thank you

 

Fred

 

De : Scott Cain [mailto:[hidden email]]
Envoyé : vendredi 28 avril 2017 16:38
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Add a Header and Footer option ?

 

Hi Fred,

 

I didn't turn on the "classic menu" in the S3 JBrowse because I wanted to touch the config as little as possible while I was debugging, but I agree, having that on is more of a bare minimum.  At WormBase, we have a header and footer on JBrowse:

 

 

Since the JBrowse page is a "simple" html index file, we just edited it until it looked more or less the way we wanted it (I toyed with the idea of making the index file an index.shtml file and doing the header and footer via includes but decided it wasn't worth the effort).  Now, I can say that I don't particularly like the result--particularly the footer.  To make the footer appear, I had to make the div that JBrowse appeared in have a fixed height, which means that some times, users have to scroll inside the JBrowse div to see content.  Since I don't like that for a user interface, I also provide a button ("Full page") that lets users switch to a JBrowse view without any of the header or footers.  If I didn't have a mandate to include the footer, I would have just gone with a header.

 

Anyway, all of this is to say that there is a fundamental difference between GBrowse and JBrowse in this regard: in GBrowse, you really need the header and footer options in the config, since the cgi is creating the page and there is no other way to inject content into the page other than via the cgi code.  With JBrowse, since the code is in an html page, you can just edit it to look the way you want, so I don't think it's necessary to have those options in the config.

 

Scott

 

 

On Fri, Apr 28, 2017 at 3:32 AM, SAPET, Frederic <[hidden email]> wrote:

Hello

 

We were using GBrowse a lot. We set up now JBrowse instead.

And there are some useful and convenient functionalities that are missing within JBrowse.

 

Is there a way to add easily a Footer and Header just like in GBrowse configuration file ?

Right now it’s not so easy for a user to guess which genome is currently displayed.

aboutThisBrowser→description is not enough, you have to click in order to get the information.

 

ie : if I want to browse the JBrowse set up by Scott in his last message to the list ( http://agrjbrowsestatic.s3-website-us-east-1.amazonaws.com/) how can I guess the genome used as reference ? There is no Citation for the reference track. The only way is maybe to look the URL, or try to guess using the prefix in chromosomes names or blast a piece of the sequence J

 

To date I have used the dataset selector but again it’s not as clear and simple as a Header.

 

Thank you.

 

Fred

 

---

Frederic Sapet

Bioinformatics Research Engineer

BIOGEMMA - Upstream Genomics Group

Centre de Recherche de Chappes

CS 90126

63720 CHAPPES

FRANCE

Tel : <a href="tel:&#43;33%204%2073%2067%2088%2054" target="_blank">+33 (0)4 73 67 88 54

Fax : <a href="tel:&#43;33%204%2073%2067%2088%2099" target="_blank">+33 (0)4 73 67 88 99

E-mail : [hidden email]

 


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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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: Add a Header and Footer option ?

Keiran Raine

Hi Fred,

 

You want

 

"classicMenu": true

 

in the base layer of jbrowse_conf.json

 

or uncomment it in jbrowse.conf.

 

Regards,

 

Keiran Raine

Principal Bioinformatician

Cancer Genome Project

Wellcome Trust Sanger Institute

 

[hidden email]

Tel:+44 (0)1223 834244 Ext: 4983

Office: H104

 

From: "SAPET, Frederic" <[hidden email]>
Date: Tuesday, 2 May 2017 at 09:27
To: Scott Cain <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [Gmod-ajax] Add a Header and Footer option ?

 

Hi Scott

 

sorry I didn't mean that your browser was poorly configured, I use it as example because it's freely accessible. my own browsers cannot be accessed publicly (and are basically configured)

 

For my purpose, modifying the index.html is not my favorite solution.

I prefer a solution related to the trackList file. indeed I would like to have an unique header for each genome (maybe something like that, with a karyotype - http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). The index.html will give me one header for all of them, right ?

by the way, the dataset selector could be enough. But how can I display the name of the current genome ?  Right now, it shows "Genome". When I click I see "Open sequence file" and the list of my configured genomes.

 

Thank you

 

Fred

 

De : Scott Cain [mailto:[hidden email]]
Envoyé : vendredi 28 avril 2017 16:38
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Add a Header and Footer option ?

 

Hi Fred,

 

I didn't turn on the "classic menu" in the S3 JBrowse because I wanted to touch the config as little as possible while I was debugging, but I agree, having that on is more of a bare minimum.  At WormBase, we have a header and footer on JBrowse:

 

 

Since the JBrowse page is a "simple" html index file, we just edited it until it looked more or less the way we wanted it (I toyed with the idea of making the index file an index.shtml file and doing the header and footer via includes but decided it wasn't worth the effort).  Now, I can say that I don't particularly like the result--particularly the footer.  To make the footer appear, I had to make the div that JBrowse appeared in have a fixed height, which means that some times, users have to scroll inside the JBrowse div to see content.  Since I don't like that for a user interface, I also provide a button ("Full page") that lets users switch to a JBrowse view without any of the header or footers.  If I didn't have a mandate to include the footer, I would have just gone with a header.

 

Anyway, all of this is to say that there is a fundamental difference between GBrowse and JBrowse in this regard: in GBrowse, you really need the header and footer options in the config, since the cgi is creating the page and there is no other way to inject content into the page other than via the cgi code.  With JBrowse, since the code is in an html page, you can just edit it to look the way you want, so I don't think it's necessary to have those options in the config.

 

Scott

 

 

On Fri, Apr 28, 2017 at 3:32 AM, SAPET, Frederic <[hidden email]> wrote:

Hello

 

We were using GBrowse a lot. We set up now JBrowse instead.

And there are some useful and convenient functionalities that are missing within JBrowse.

 

Is there a way to add easily a Footer and Header just like in GBrowse configuration file ?

Right now it’s not so easy for a user to guess which genome is currently displayed.

aboutThisBrowser→description is not enough, you have to click in order to get the information.

 

ie : if I want to browse the JBrowse set up by Scott in his last message to the list ( http://agrjbrowsestatic.s3-website-us-east-1.amazonaws.com/) how can I guess the genome used as reference ? There is no Citation for the reference track. The only way is maybe to look the URL, or try to guess using the prefix in chromosomes names or blast a piece of the sequence J

 

To date I have used the dataset selector but again it’s not as clear and simple as a Header.

 

Thank you.

 

Fred

 

---

Frederic Sapet

Bioinformatics Research Engineer

BIOGEMMA - Upstream Genomics Group

Centre de Recherche de Chappes

CS 90126

63720 CHAPPES

FRANCE

Tel : <a href="tel:&#43;33%204%2073%2067%2088%2054" target="_blank"> +33 (0)4 73 67 88 54

Fax : <a href="tel:&#43;33%204%2073%2067%2088%2099" target="_blank"> +33 (0)4 73 67 88 99

E-mail : [hidden email]

 


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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

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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Re: Add a Header and Footer option ?

FredBGA

Hi Keiran

 

Nice, thank you.

It’s obvious now,  in the configuration file.

## use classic jbrowse menu with file instead of track and genome

 

It works of course and will fulfill my basic needs.

 

Fred

 

De : Keiran Raine [mailto:[hidden email]]
Envoyé : mardi 2 mai 2017 13:06
À : SAPET, Frederic <[hidden email]>; Scott Cain <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Add a Header and Footer option ?

 

Hi Fred,

 

You want

 

"classicMenu": true

 

in the base layer of jbrowse_conf.json

 

or uncomment it in jbrowse.conf.

 

Regards,

 

Keiran Raine

Principal Bioinformatician

Cancer Genome Project

Wellcome Trust Sanger Institute

 

[hidden email]

<a href="Tel:&#43;44">Tel:+44 (0)1223 834244 Ext: 4983

Office: H104

 

From: "SAPET, Frederic" <[hidden email]>
Date: Tuesday, 2 May 2017 at 09:27
To: Scott Cain <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [Gmod-ajax] Add a Header and Footer option ?

 

Hi Scott

 

sorry I didn't mean that your browser was poorly configured, I use it as example because it's freely accessible. my own browsers cannot be accessed publicly (and are basically configured)

 

For my purpose, modifying the index.html is not my favorite solution.

I prefer a solution related to the trackList file. indeed I would like to have an unique header for each genome (maybe something like that, with a karyotype - http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). The index.html will give me one header for all of them, right ?

by the way, the dataset selector could be enough. But how can I display the name of the current genome ?  Right now, it shows "Genome". When I click I see "Open sequence file" and the list of my configured genomes.

 

Thank you

 

Fred

 

De : Scott Cain [[hidden email]]
Envoyé : vendredi 28 avril 2017 16:38
À : SAPET, Frederic <
[hidden email]>
Cc :
[hidden email]
Objet : Re: [Gmod-ajax] Add a Header and Footer option ?

 

Hi Fred,

 

I didn't turn on the "classic menu" in the S3 JBrowse because I wanted to touch the config as little as possible while I was debugging, but I agree, having that on is more of a bare minimum.  At WormBase, we have a header and footer on JBrowse:

 

 

Since the JBrowse page is a "simple" html index file, we just edited it until it looked more or less the way we wanted it (I toyed with the idea of making the index file an index.shtml file and doing the header and footer via includes but decided it wasn't worth the effort).  Now, I can say that I don't particularly like the result--particularly the footer.  To make the footer appear, I had to make the div that JBrowse appeared in have a fixed height, which means that some times, users have to scroll inside the JBrowse div to see content.  Since I don't like that for a user interface, I also provide a button ("Full page") that lets users switch to a JBrowse view without any of the header or footers.  If I didn't have a mandate to include the footer, I would have just gone with a header.

 

Anyway, all of this is to say that there is a fundamental difference between GBrowse and JBrowse in this regard: in GBrowse, you really need the header and footer options in the config, since the cgi is creating the page and there is no other way to inject content into the page other than via the cgi code.  With JBrowse, since the code is in an html page, you can just edit it to look the way you want, so I don't think it's necessary to have those options in the config.

 

Scott

 

 

On Fri, Apr 28, 2017 at 3:32 AM, SAPET, Frederic <[hidden email]> wrote:

Hello

 

We were using GBrowse a lot. We set up now JBrowse instead.

And there are some useful and convenient functionalities that are missing within JBrowse.

 

Is there a way to add easily a Footer and Header just like in GBrowse configuration file ?

Right now it’s not so easy for a user to guess which genome is currently displayed.

aboutThisBrowser→description is not enough, you have to click in order to get the information.

 

ie : if I want to browse the JBrowse set up by Scott in his last message to the list ( http://agrjbrowsestatic.s3-website-us-east-1.amazonaws.com/) how can I guess the genome used as reference ? There is no Citation for the reference track. The only way is maybe to look the URL, or try to guess using the prefix in chromosomes names or blast a piece of the sequence J

 

To date I have used the dataset selector but again it’s not as clear and simple as a Header.

 

Thank you.

 

Fred

 

---

Frederic Sapet

Bioinformatics Research Engineer

BIOGEMMA - Upstream Genomics Group

Centre de Recherche de Chappes

CS 90126

63720 CHAPPES

FRANCE

Tel : <a href="tel:&#43;33%204%2073%2067%2088%2054" target="_blank">+33 (0)4 73 67 88 54

Fax : <a href="tel:&#43;33%204%2073%2067%2088%2099" target="_blank">+33 (0)4 73 67 88 99

E-mail : [hidden email]

 


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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

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.


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