gbrowse_img under 2.17

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gbrowse_img under 2.17

Benjamin Hitz

So, I have been wrestling with gbrowse_img for a couple days now.
First off - the docs are in error:

----
type (Alias: t)
This argument lists the feature types to display. The value of this argument is a list of track names separated by spaces ("+" characters when URL-escaped). For example:
      <img src="http://www.wormbase.org/db/seq/gbrowse_img/c_elegans?name=mec-3;
                   type=tRNA+NG+WABA+CG+ESTB">
     

Multiple type= arguments will be combined to form a single space-delimited list. The alias "t" can be used to shorten the length of the URL.
If the track name has a space in it, put quotes around the name:

            type="microbe tRNA"+NG+WABA+CG+ESTB
-----

Using spaces or "+" or "%20" to separate tracks doesn't work in my hands (2.17bugfix branch).  Luckily having multiple type=X;type=Y does work.  



Second - I get a 60px white border on the RHS of all my images.  Compare:

Gbrowse 2.17




Gbrowse 1.68 (what can I say, we are not early adopters)





I would really prefer to NOT have to run all my gbrowse_img (we cache them) through an image processor... is there some flag that fixes this?

In addition, I would like to remove the Track header "Everything", but I presume that is a config issue.  Reporting the coord range at the top I might keep although I didn't do it on purpose.

Ben
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]




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Re: gbrowse_img under 2.17

Jayaraman, Pushkala
I second that. I have been using multiple key value pairs with "type" as
key for each of the additional tracks I wish to display in my
gbrowse_img.. I guessed that was an alternate behavior! :)

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Benjamin Hitz [mailto:[hidden email]]
Sent: Friday, January 21, 2011 12:07 PM
To: [hidden email]
Subject: [Gmod-gbrowse] gbrowse_img under 2.17


So, I have been wrestling with gbrowse_img for a couple days now.
First off - the docs are in error:

----
type (Alias: t)
This argument lists the feature types to display. The value of this
argument is a list of track names separated by spaces ("+" characters
when URL-escaped). For example:
      <img
src="http://www.wormbase.org/db/seq/gbrowse_img/c_elegans?name=mec-3;
                   type=tRNA+NG+WABA+CG+ESTB">
     

Multiple type= arguments will be combined to form a single
space-delimited list. The alias "t" can be used to shorten the length of
the URL.
If the track name has a space in it, put quotes around the name:

            type="microbe tRNA"+NG+WABA+CG+ESTB
-----

Using spaces or "+" or "%20" to separate tracks doesn't work in my hands
(2.17bugfix branch).  Luckily having multiple type=X;type=Y does work.




Second - I get a 60px white border on the RHS of all my images.
Compare:

Gbrowse 2.17


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February 28th, so secure your free ArcSight Logger TODAY!
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Re: gbrowse_img under 2.17

Benjamin Hitz

Well, I did find that I had pad_left set to 60. I guess the old gbrowse_img ignored this; not even sure what the provenance of this is the config.
So it's just as well that my images didn't show up.

Haven't found the magic button to turn off track name yet, but still looking.

Ben

On Jan 21, 2011, at 10:20 AM, Jayaraman, Pushkala wrote:

> I second that. I have been using multiple key value pairs with "type" as
> key for each of the additional tracks I wish to display in my
> gbrowse_img.. I guessed that was an alternate behavior! :)
>
>
> Second - I get a 60px white border on the RHS of all my images.
> Compare:
>
> Gbrowse 2.17
>

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]




------------------------------------------------------------------------------
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Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
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Re: gbrowse_img under 2.17

Benjamin Hitz
>
>
> Haven't found the magic button to turn off track name yet, but still looking.

For the sake of future generations, if you put
key            =

(that's no characters, no quotes) then it shows no Title for a track.

Also, I don't know if this is a bug or feature but
pad_left = X
doesn't seem to be over-ridable.

It's set in GBrowse.conf (the file with the source definitions, etc.) , and the individual conf files can't override it by setting pad_left = Y

Ben

>
> Ben
>
> On Jan 21, 2011, at 10:20 AM, Jayaraman, Pushkala wrote:
>
>> I second that. I have been using multiple key value pairs with "type" as
>> key for each of the additional tracks I wish to display in my
>> gbrowse_img.. I guessed that was an alternate behavior! :)
>>
>>
>> Second - I get a 60px white border on the RHS of all my images.
>> Compare:
>>
>> Gbrowse 2.17
>>
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> Stanford University ** [hidden email]
>
>
>

--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




------------------------------------------------------------------------------
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Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
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Re: gbrowse_img under 2.17

Lincoln Stein
In reply to this post by Benjamin Hitz
Hi,

I'll take a look at this; the software should work in the way
described by the docs.

Lincoln

On Friday, January 21, 2011, Benjamin Hitz <[hidden email]> wrote:

>
> So, I have been wrestling with gbrowse_img for a couple days now.
> First off - the docs are in error:
>
> ----
> type (Alias: t)
> This argument lists the feature types to display. The value of this argument is a list of track names separated by spaces ("+" characters when URL-escaped). For example:
>       <img src="http://www.wormbase.org/db/seq/gbrowse_img/c_elegans?name=mec-3;
>                    type=tRNA+NG+WABA+CG+ESTB">
>
>
> Multiple type= arguments will be combined to form a single space-delimited list. The alias "t" can be used to shorten the length of the URL.
> If the track name has a space in it, put quotes around the name:
>
>             type="microbe tRNA"+NG+WABA+CG+ESTB
> -----
>
> Using spaces or "+" or "%20" to separate tracks doesn't work in my hands (2.17bugfix branch).  Luckily having multiple type=X;type=Y does work.
>
>
>
> Second - I get a 60px white border on the RHS of all my images.  Compare:
>
> Gbrowse 2.17
>
>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
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Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
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Re: gbrowse_img under 2.17

Ellen Adlem
I was trying to get gbrowse_img working as per the docs but the docs
that are included bit they seem to be written for GB 1.X rather than
2.X.  Is there a version of docs for gbrowse_img written for 2.X
anywhere please?

Specifically, h_feat & keystyle don't seem to work as per the documentation.

Cheers.

Ellen.

--
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215


On 24/01/11 17:03, Lincoln Stein wrote:

> Hi,
>
> I'll take a look at this; the software should work in the way
> described by the docs.
>
> Lincoln
>
> On Friday, January 21, 2011, Benjamin Hitz<[hidden email]>  wrote:
>> So, I have been wrestling with gbrowse_img for a couple days now.
>> First off - the docs are in error:
>>
>> ----
>> type (Alias: t)
>> This argument lists the feature types to display. The value of this argument is a list of track names separated by spaces ("+" characters when URL-escaped). For example:
>>        <img src="http://www.wormbase.org/db/seq/gbrowse_img/c_elegans?name=mec-3;
>>                     type=tRNA+NG+WABA+CG+ESTB">
>>
>>
>> Multiple type= arguments will be combined to form a single space-delimited list. The alias "t" can be used to shorten the length of the URL.
>> If the track name has a space in it, put quotes around the name:
>>
>>              type="microbe tRNA"+NG+WABA+CG+ESTB
>> -----
>>
>> Using spaces or "+" or "%20" to separate tracks doesn't work in my hands (2.17bugfix branch).  Luckily having multiple type=X;type=Y does work.
>>
>>
>>
>> Second - I get a 60px white border on the RHS of all my images.  Compare:
>>
>> Gbrowse 2.17
>>
>>

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Re: gbrowse_img under 2.17

Lincoln Stein
Hi Ellen,

2.X gbrowse_img is supposed to work as documented for 1.X, so your problems are likely bugs. Could you file a bug report at www.sourceforge.net/projects/gmod?

I can see why keystyle wouldn't work properly due to the change in the track rendering architecture. Are you trying to create a key at the bottom of the panel?

Lincoln

On Mon, Feb 14, 2011 at 11:54 AM, Ellen Adlem <[hidden email]> wrote:
I was trying to get gbrowse_img working as per the docs but the docs that are included bit they seem to be written for GB 1.X rather than 2.X.  Is there a version of docs for gbrowse_img written for 2.X anywhere please?

Specifically, h_feat & keystyle don't seem to work as per the documentation.

Cheers.

Ellen.

--
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215



On 24/01/11 17:03, Lincoln Stein wrote:
Hi,

I'll take a look at this; the software should work in the way
described by the docs.

Lincoln

On Friday, January 21, 2011, Benjamin Hitz<[hidden email]>  wrote:
So, I have been wrestling with gbrowse_img for a couple days now.
First off - the docs are in error:

----
type (Alias: t)
This argument lists the feature types to display. The value of this argument is a list of track names separated by spaces ("+" characters when URL-escaped). For example:
      <img src="http://www.wormbase.org/db/seq/gbrowse_img/c_elegans?name=mec-3;
                   type=tRNA+NG+WABA+CG+ESTB">


Multiple type= arguments will be combined to form a single space-delimited list. The alias "t" can be used to shorten the length of the URL.
If the track name has a space in it, put quotes around the name:

            type="microbe tRNA"+NG+WABA+CG+ESTB
-----

Using spaces or "+" or "%20" to separate tracks doesn't work in my hands (2.17bugfix branch).  Luckily having multiple type=X;type=Y does work.



Second - I get a 60px white border on the RHS of all my images.  Compare:

Gbrowse 2.17





--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
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Re: gbrowse_img under 2.17

Ellen Adlem
Many thanks Lincoln.

I tried v2.25 today to confirm the status and h_feat is still not working so have created a bug on the SF tracker.

Cheers.
Ellen.
-- 
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215

On 14/02/11 17:02, Lincoln Stein wrote:
Hi Ellen,

2.X gbrowse_img is supposed to work as documented for 1.X, so your problems are likely bugs. Could you file a bug report at www.sourceforge.net/projects/gmod?

I can see why keystyle wouldn't work properly due to the change in the track rendering architecture. Are you trying to create a key at the bottom of the panel?

Lincoln

On Mon, Feb 14, 2011 at 11:54 AM, Ellen Adlem <[hidden email]> wrote:
I was trying to get gbrowse_img working as per the docs but the docs that are included bit they seem to be written for GB 1.X rather than 2.X.  Is there a version of docs for gbrowse_img written for 2.X anywhere please?

Specifically, h_feat & keystyle don't seem to work as per the documentation.

Cheers.

Ellen.

--
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215



On 24/01/11 17:03, Lincoln Stein wrote:
Hi,

I'll take a look at this; the software should work in the way
described by the docs.

Lincoln

On Friday, January 21, 2011, Benjamin Hitz<[hidden email]>  wrote:
So, I have been wrestling with gbrowse_img for a couple days now.
First off - the docs are in error:

----
type (Alias: t)
This argument lists the feature types to display. The value of this argument is a list of track names separated by spaces ("+" characters when URL-escaped). For example:
      <img src="http://www.wormbase.org/db/seq/gbrowse_img/c_elegans?name=mec-3;
                   type=tRNA+NG+WABA+CG+ESTB">


Multiple type= arguments will be combined to form a single space-delimited list. The alias "t" can be used to shorten the length of the URL.
If the track name has a space in it, put quotes around the name:

            type="microbe tRNA"+NG+WABA+CG+ESTB
-----

Using spaces or "+" or "%20" to separate tracks doesn't work in my hands (2.17bugfix branch).  Luckily having multiple type=X;type=Y does work.



Second - I get a 60px white border on the RHS of all my images.  Compare:

Gbrowse 2.17





--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse