GBrowse 2.22 released

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GBrowse 2.22 released

Lincoln Stein
Hi All,

I have just released GBrowse version 2.22 to CPAN. It is a minor bugfix maintenance release which fixes two bugs:

  • The "eurl" param, which is used to load remote URLs as custom tracks via the GBrowse URL now works when user accounts are disabled.
  • gbrowse_img has been fixed so that you can activate multiple tracks with the URL parameter "t=track1+track2+track3".
Lincoln

--
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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Re: GBrowse 2.22 released

Keiran Raine
Hi Lincoln,

Just tried to install to our test server and noticed this during the tests:

t/03.render.t ............. 138/150 Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN165> line 2.

Installation appears to be successful though.

I noticed that when clicking on the DNA track I get the result shown in the attached image, even though, as shown by the co-ordinates, only 30 b.p. have been requested.  When looking at the error log I find that each request to the gbrowse_detail page for this request results in the following:

Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN5> line 2.

My Bioperl install was generated using this archive:

bioperl-bioperl-live-bioperl-release-1-5-1-rc4-4147-g3a03b23.tar.gz

Kind regards

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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Finally, a world-class log management solution at an even better price-free!
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February 28th, so secure your free ArcSight Logger TODAY!
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Re: GBrowse 2.22 released

Scott Cain
Keiran,

Are you really using bioperl 1.5.1?  That is really old.

Scott


On Thu, Jan 27, 2011 at 8:29 AM, Keiran Raine <[hidden email]> wrote:
Hi Lincoln,

Just tried to install to our test server and noticed this during the tests:

t/03.render.t ............. 138/150 Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN165> line 2.

Installation appears to be successful though.

I noticed that when clicking on the DNA track I get the result shown in the attached image, even though, as shown by the co-ordinates, only 30 b.p. have been requested.  When looking at the error log I find that each request to the gbrowse_detail page for this request results in the following:

Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN5> line 2.

My Bioperl install was generated using this archive:

bioperl-bioperl-live-bioperl-release-1-5-1-rc4-4147-g3a03b23.tar.gz

Kind regards

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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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--
------------------------------------------------------------------------
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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Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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 2.22 released

Keiran Raine
Nope, actually that's just me being dense.

bioperl-bioperl-live-3a03b23 (1.6.1_1)

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 27 Jan 2011, at 13:38, Scott Cain wrote:

Keiran,

Are you really using bioperl 1.5.1?  That is really old.

Scott


On Thu, Jan 27, 2011 at 8:29 AM, Keiran Raine <[hidden email]> wrote:
Hi Lincoln,

Just tried to install to our test server and noticed this during the tests:

t/03.render.t ............. 138/150 Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN165> line 2.

Installation appears to be successful though.

I noticed that when clicking on the DNA track I get the result shown in the attached image, even though, as shown by the co-ordinates, only 30 b.p. have been requested.  When looking at the error log I find that each request to the gbrowse_detail page for this request results in the following:

Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN5> line 2.

My Bioperl install was generated using this archive:

bioperl-bioperl-live-bioperl-release-1-5-1-rc4-4147-g3a03b23.tar.gz

Kind regards

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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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--
------------------------------------------------------------------------
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 compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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 2.22 released

Lincoln Stein
In reply to this post by Keiran Raine
Hi Keiran,

This is a long standing bug in how gbrowse_details handles global features that has been present since 1.5. If it is bothering you I will fix it.

I noticed the pack warnings too, but the cause appears to be related to more strict warnings in later versions of Perl. They are innocuous but require a bioperl update.

Lincoln

On 2011-01-27, at 8:29 AM, Keiran Raine <[hidden email]> wrote:

Hi Lincoln,

Just tried to install to our test server and noticed this during the tests:

t/03.render.t ............. 138/150 Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN165> line 2.

Installation appears to be successful though.

I noticed that when clicking on the DNA track I get the result shown in the attached image, even though, as shown by the co-ordinates, only 30 b.p. have been requested.  When looking at the error log I find that each request to the gbrowse_detail page for this request results in the following:

Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN5> line 2.

My Bioperl install was generated using this archive:

bioperl-bioperl-live-bioperl-release-1-5-1-rc4-4147-g3a03b23.tar.gz

Kind regards

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703

<Picture 12.png>
-- 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.

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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 2.22 released

Keiran Raine
On 27 Jan 2011, at 18:07, Lincoln Stein wrote:

Hi Keiran,

This is a long standing bug in how gbrowse_details handles global features that has been present since 1.5. If it is bothering you I will fix it.

It would be quite a useful feature for our PostDocs to pull out the sequence context of mutations more easily (instead of fasta download etc).  However as they don't know it can do this It's not urgent.


I noticed the pack warnings too, but the cause appears to be related to more strict warnings in later versions of Perl. They are innocuous but require a bioperl update.

Ok, I could not remember seeing it previously.


Lincoln

On 2011-01-27, at 8:29 AM, Keiran Raine <[hidden email]> wrote:

Hi Lincoln,

Just tried to install to our test server and noticed this during the tests:

t/03.render.t ............. 138/150 Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN165> line 2.

Installation appears to be successful though.

I noticed that when clicking on the DNA track I get the result shown in the attached image, even though, as shown by the co-ordinates, only 30 b.p. have been requested.  When looking at the error log I find that each request to the gbrowse_detail page for this request results in the following:

Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN5> line 2.

My Bioperl install was generated using this archive:

bioperl-bioperl-live-bioperl-release-1-5-1-rc4-4147-g3a03b23.tar.gz

Kind regards

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703

<Picture 12.png>
-- 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.


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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 2.22 released

Keiran Raine
In reply to this post by Lincoln Stein
Hi Lincoln,

Below I raised a problem you were already aware of on the DNA track not showing sequence within the gbrowse_detail page.  I have since found that I am unable to save the FASTA for the region of a DNA displayed via the 'Download this track' option (I get an empty file).

I'm sure this used to work for the DNA track (within GBrowse 2+).  Is this a new problem?

FYI - tested on 2.24 since this thread was started.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 27 Jan 2011, at 18:07, Lincoln Stein wrote:

Hi Keiran,

This is a long standing bug in how gbrowse_details handles global features that has been present since 1.5. If it is bothering you I will fix it.

I noticed the pack warnings too, but the cause appears to be related to more strict warnings in later versions of Perl. They are innocuous but require a bioperl update.

Lincoln

On 2011-01-27, at 8:29 AM, Keiran Raine <[hidden email]> wrote:

Hi Lincoln,

Just tried to install to our test server and noticed this during the tests:

t/03.render.t ............. 138/150 Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN165> line 2.

Installation appears to be successful though.

I noticed that when clicking on the DNA track I get the result shown in the attached image, even though, as shown by the co-ordinates, only 30 b.p. have been requested.  When looking at the error log I find that each request to the gbrowse_detail page for this request results in the following:

Use of uninitialized value $_[4] in pack at /gbrowse/share/perl/5.10.0/Bio/DB/Fasta.pm line 989, <GEN5> line 2.

My Bioperl install was generated using this archive:

bioperl-bioperl-live-bioperl-release-1-5-1-rc4-4147-g3a03b23.tar.gz

Kind regards

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703

<Picture 12.png>
-- 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.


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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
_______________________________________________
Gmod-gbrowse mailing list
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