Bernd Jagla | 1 Mar 13:14 2010
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Picon

biodas for GBrowse 2

Hi,

 

Lincoln told me that BioDas needs to be ported from GB1 to GB2. Is there a plan for doing so? Is there a targeted release date? What needs to be done? Could I do this with my “limited” Perl / Bioperl knowledge?

If you tell me what needs to be done and which tests need to be working I would be willing to give it a try…

 

Thanks

 

Bernd

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Scott Perry | 1 Mar 14:41 2010
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Re: biodas for GBrowse 2

Hi Bernd,

Maybe this will help.. I played around with DAS a few months ago and managed to get UCSC tracks to show up by making the following changes:

1. In RenderPanels::get_iterator:

This method was generating exceptions because Bio::Das doesn't
actually implement 'get_seq_stream'. I just added a quick check to the
if statement at the beginning of the method:

if ($db->can('get_seq_stream') && !$db->isa("Bio::Das")) { ...

2. In Bio::Das::Request::Features::

finish_segment:  I had to  comment
out the following line. It was unnecessarily encapsulating all of the
results in 'group' features.

$self->infer_parents_from_groups($self->{tmp}{features});


Let me know if you need any more info and I'll send you the diff.

-Scott

On Mon, Mar 1, 2010 at 8:14 AM, Bernd Jagla <bernd.jagla-M1hYzG+5fJxGWvitb5QawA@public.gmane.org> wrote:

Hi,

 

Lincoln told me that BioDas needs to be ported from GB1 to GB2. Is there a plan for doing so? Is there a targeted release date? What needs to be done? Could I do this with my “limited” Perl / Bioperl knowledge?

If you tell me what needs to be done and which tests need to be working I would be willing to give it a try…

 

Thanks

 

Bernd


------------------------------------------------------------------------------
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Syed Mustafa Hussain | 1 Mar 17:01 2010
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Re: adding new glyph to library

Lincoln,

I have Bio::Graphics libraries at several different places, and I have no control over installation. I
think our system administrator had to make these additional libraries because Bio/Graphics were not
supplied as part of Bioperl later. Where can I find which library Gbrowse is using?

Following are the places where I can find Bio/Graphics:

/usr/lib/perl5/site_perl/5.8.8/Bio/Graphics

/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics

/usr/local/Generic-Genome-Browser-1.69/lib/Bio/Graphics/

/usr/local/Generic-Genome-Browser-1.69/blib/lib/Bio/Graphics

Thanks,
Mustafa.

--- On Sat, 2/27/10, Lincoln Stein <lincoln.stein@...> wrote:

> From: Lincoln Stein <lincoln.stein@...>
> Subject: Re: [Gmod-gbrowse] adding new glyph to library
> To: "Syed Mustafa Hussain" <comp_sea@...>
> Cc: gmod-gbrowse@...
> Date: Saturday, February 27, 2010, 3:41 AM
> You need to copy the glyph.pm file
> into the appropriate library in your perl search path.
> Neither of these paths look right.
> Lincoln
> 
> On Fri, Feb 26, 2010 at 4:26 PM,
> Syed Mustafa Hussain <comp_sea@...>
> wrote:
> 
> 
> 
> Hi,
> 
> 
> 
> I want to add allele_column_multi glyph to glyph library. I
> have copied module to both bioperl Bio::Graphics::Glyphs
> library and lib inside
> /usr/local/Generic-Genome-Browser-1.69/lib and I have in
> config file:
> 
> 
> 
> [SNP:50]
> 
> feature        = SNP
> 
> glyph          = allele_column_multi
> 
> alleles        = A/T
> 
> majorcolor     = blue
> 
> minorcolor     = red
> 
> ref_strand     = '+'
> 
> freq           =
> 'ASW:0.3;CEU:0.6;CHB:0.4;CHD:0.5'
> 
> 
> 
> But I do not see any image in detail panel. If I substitute
> allele_column_multi glyph with some other glyph it is
> visible.
> 
> 
> 
> Whatelse I need to do to make it appear. What is the
> procedure to add new glyph.
> 
> 
> 
> Thanks,
> 
> Mustafa.
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> 
> Download Intel® Parallel Studio Eval
> 
> Try the new software tools for yourself. Speed compiling,
> find bugs
> 
> proactively, and fine-tune applications for parallel
> performance.
> 
> See why Intel Parallel Studio got high marks during beta.
> 
> http://p.sf.net/sfu/intel-sw-dev
> 
> _______________________________________________
> 
> Gmod-gbrowse mailing list
> 
> Gmod-gbrowse@...
> 
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> 
> 
> 
> 
> -- 
> 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 <Renata.Musa@...>
> 
> 
> 

------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Syed Mustafa Hussain | 1 Mar 17:17 2010
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Re: adding new glyph to library

Lincoln,

Glyph.pm might not be a problem as other glyphs including "allele_tower" are showing up. 

error_log is showing only this error:

..... Bio::Graphics::BrowserConfig=HASH(0x1c25930) at
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 587., .....

Thanks,
Mustafa.

--- On Sat, 2/27/10, Lincoln Stein <lincoln.stein@...> wrote:

> From: Lincoln Stein <lincoln.stein@...>
> Subject: Re: [Gmod-gbrowse] adding new glyph to library
> To: "Syed Mustafa Hussain" <comp_sea@...>
> Cc: gmod-gbrowse@...
> Date: Saturday, February 27, 2010, 3:41 AM
> You need to copy the glyph.pm file
> into the appropriate library in your perl search path.
> Neither of these paths look right.
> Lincoln
> 
> On Fri, Feb 26, 2010 at 4:26 PM,
> Syed Mustafa Hussain <comp_sea@...>
> wrote:
> 
> 
> 
> Hi,
> 
> 
> 
> I want to add allele_column_multi glyph to glyph library. I
> have copied module to both bioperl Bio::Graphics::Glyphs
> library and lib inside
> /usr/local/Generic-Genome-Browser-1.69/lib and I have in
> config file:
> 
> 
> 
> [SNP:50]
> 
> feature        = SNP
> 
> glyph          = allele_column_multi
> 
> alleles        = A/T
> 
> majorcolor     = blue
> 
> minorcolor     = red
> 
> ref_strand     = '+'
> 
> freq           =
> 'ASW:0.3;CEU:0.6;CHB:0.4;CHD:0.5'
> 
> 
> 
> But I do not see any image in detail panel. If I substitute
> allele_column_multi glyph with some other glyph it is
> visible.
> 
> 
> 
> Whatelse I need to do to make it appear. What is the
> procedure to add new glyph.
> 
> 
> 
> Thanks,
> 
> Mustafa.
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> 
> Download Intel® Parallel Studio Eval
> 
> Try the new software tools for yourself. Speed compiling,
> find bugs
> 
> proactively, and fine-tune applications for parallel
> performance.
> 
> See why Intel Parallel Studio got high marks during beta.
> 
> http://p.sf.net/sfu/intel-sw-dev
> 
> _______________________________________________
> 
> Gmod-gbrowse mailing list
> 
> Gmod-gbrowse@...
> 
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> 
> 
> 
> 
> -- 
> 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 <Renata.Musa@...>
> 
> 
> 

------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
Scott Cain | 1 Mar 17:22 2010
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Re: adding new glyph to library

Hi Mustafa,

The message is a debugging message that was inadvertantantly left in
the 1.69 release, and you can ignore it, so that isn't informative at
all.

Sorry,
Scott

On Mon, Mar 1, 2010 at 11:17 AM, Syed Mustafa Hussain
<comp_sea@...> wrote:
> Lincoln,
>
> Glyph.pm might not be a problem as other glyphs including "allele_tower" are showing up.
>
> error_log is showing only this error:
>
> ..... Bio::Graphics::BrowserConfig=HASH(0x1c25930) at
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 587., .....
>
> Thanks,
> Mustafa.
>
> --- On Sat, 2/27/10, Lincoln Stein <lincoln.stein@...> wrote:
>
>> From: Lincoln Stein <lincoln.stein@...>
>> Subject: Re: [Gmod-gbrowse] adding new glyph to library
>> To: "Syed Mustafa Hussain" <comp_sea@...>
>> Cc: gmod-gbrowse@...
>> Date: Saturday, February 27, 2010, 3:41 AM
>> You need to copy the glyph.pm file
>> into the appropriate library in your perl search path.
>> Neither of these paths look right.
>> Lincoln
>>
>> On Fri, Feb 26, 2010 at 4:26 PM,
>> Syed Mustafa Hussain <comp_sea@...>
>> wrote:
>>
>>
>>
>> Hi,
>>
>>
>>
>> I want to add allele_column_multi glyph to glyph library. I
>> have copied module to both bioperl Bio::Graphics::Glyphs
>> library and lib inside
>> /usr/local/Generic-Genome-Browser-1.69/lib and I have in
>> config file:
>>
>>
>>
>> [SNP:50]
>>
>> feature        = SNP
>>
>> glyph          = allele_column_multi
>>
>> alleles        = A/T
>>
>> majorcolor     = blue
>>
>> minorcolor     = red
>>
>> ref_strand     = '+'
>>
>> freq           =
>> 'ASW:0.3;CEU:0.6;CHB:0.4;CHD:0.5'
>>
>>
>>
>> But I do not see any image in detail panel. If I substitute
>> allele_column_multi glyph with some other glyph it is
>> visible.
>>
>>
>>
>> Whatelse I need to do to make it appear. What is the
>> procedure to add new glyph.
>>
>>
>>
>> Thanks,
>>
>> Mustafa.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> Download Intel® Parallel Studio Eval
>>
>> Try the new software tools for yourself. Speed compiling,
>> find bugs
>>
>> proactively, and fine-tune applications for parallel
>> performance.
>>
>> See why Intel Parallel Studio got high marks during beta.
>>
>> http://p.sf.net/sfu/intel-sw-dev
>>
>> _______________________________________________
>>
>> Gmod-gbrowse mailing list
>>
>> Gmod-gbrowse@...
>>
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>>
>> --
>> 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 <Renata.Musa@...>
>>
>>
>>
>
>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--

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

------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
Syed Mustafa Hussain | 1 Mar 19:23 2010
Picon

Re: adding new glyph to library

Thanks Scott!

Will you please suggest best way to debug this kind of problem?

Mustafa.

--- On Mon, 3/1/10, Scott Cain <scott@...> wrote:

> From: Scott Cain <scott@...>
> Subject: Re: [Gmod-gbrowse] adding new glyph to library
> To: "Syed Mustafa Hussain" <comp_sea@...>
> Cc: "Lincoln Stein" <lincoln.stein@...>, gmod-gbrowse@...orge.net
> Date: Monday, March 1, 2010, 9:52 PM
> Hi Mustafa,
> 
> The message is a debugging message that was
> inadvertantantly left in
> the 1.69 release, and you can ignore it, so that isn't
> informative at
> all.
> 
> Sorry,
> Scott
> 
> 
> On Mon, Mar 1, 2010 at 11:17 AM, Syed Mustafa Hussain
> <comp_sea@...>
> wrote:
> > Lincoln,
> >
> > Glyph.pm might not be a problem as other glyphs
> including "allele_tower" are showing up.
> >
> > error_log is showing only this error:
> >
> > ..... Bio::Graphics::BrowserConfig=HASH(0x1c25930) at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., .....
> >
> > Thanks,
> > Mustafa.
> >
> > --- On Sat, 2/27/10, Lincoln Stein <lincoln.stein@...>
> wrote:
> >
> >> From: Lincoln Stein <lincoln.stein@...>
> >> Subject: Re: [Gmod-gbrowse] adding new glyph to
> library
> >> To: "Syed Mustafa Hussain" <comp_sea@...>
> >> Cc: gmod-gbrowse@...
> >> Date: Saturday, February 27, 2010, 3:41 AM
> >> You need to copy the glyph.pm file
> >> into the appropriate library in your perl search
> path.
> >> Neither of these paths look right.
> >> Lincoln
> >>
> >> On Fri, Feb 26, 2010 at 4:26 PM,
> >> Syed Mustafa Hussain <comp_sea@...>
> >> wrote:
> >>
> >>
> >>
> >> Hi,
> >>
> >>
> >>
> >> I want to add allele_column_multi glyph to glyph
> library. I
> >> have copied module to both bioperl
> Bio::Graphics::Glyphs
> >> library and lib inside
> >> /usr/local/Generic-Genome-Browser-1.69/lib and I
> have in
> >> config file:
> >>
> >>
> >>
> >> [SNP:50]
> >>
> >> feature        = SNP
> >>
> >> glyph          = allele_column_multi
> >>
> >> alleles        = A/T
> >>
> >> majorcolor     = blue
> >>
> >> minorcolor     = red
> >>
> >> ref_strand     = '+'
> >>
> >> freq           =
> >> 'ASW:0.3;CEU:0.6;CHB:0.4;CHD:0.5'
> >>
> >>
> >>
> >> But I do not see any image in detail panel. If I
> substitute
> >> allele_column_multi glyph with some other glyph it
> is
> >> visible.
> >>
> >>
> >>
> >> Whatelse I need to do to make it appear. What is
> the
> >> procedure to add new glyph.
> >>
> >>
> >>
> >> Thanks,
> >>
> >> Mustafa.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >>
> >> Download Intel® Parallel Studio Eval
> >>
> >> Try the new software tools for yourself. Speed
> compiling,
> >> find bugs
> >>
> >> proactively, and fine-tune applications for
> parallel
> >> performance.
> >>
> >> See why Intel Parallel Studio got high marks
> during beta.
> >>
> >> http://p.sf.net/sfu/intel-sw-dev
> >>
> >> _______________________________________________
> >>
> >> Gmod-gbrowse mailing list
> >>
> >> Gmod-gbrowse@...
> >>
> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >>
> >>
> >>
> >>
> >> --
> >> 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 <Renata.Musa@...>
> >>
> >>
> >>
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed
> compiling, find bugs
> > proactively, and fine-tune applications for parallel
> performance.
> > See why Intel Parallel Studio got high marks during
> beta.
> > http://p.sf.net/sfu/intel-sw-dev
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse@...
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.           
>                
>        scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)         
>            216-392-3087
> Ontario Institute for Cancer Research
> 

------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
Scott Cain | 1 Mar 20:59 2010
Picon

Re: adding new glyph to library

Hi Mustafa,

Having multiple instances of Bio::Graphics makes life a little
difficult.  Could you suggest to your sysadmin that he install
Bio::Graphics with the "--uninst 1" option on the install command,
like this:

  ./Build install --uninst 1

which will remove old and unused copies of Bio::Graphics modules from
your perl path so it will be more readily obvious which one you are
using.

Failing that, you should su to the user that is running apache
(frequently named apache, nobody or www-data) and issue the perl -V
command using the perl that is being executed in the gbrowse cgi
(typically but not always /usr/bin/perl).  At the end of the output of
the perl -V command is the list of  <at> INC, the paths that perl searches
for perl modules.  Whichever one of those that is first when looking
at the list of places where Bio::Graphics is installed is the one that
gbrowse is using.

Scott

On Mon, Mar 1, 2010 at 1:23 PM, Syed Mustafa Hussain
<comp_sea@...> wrote:
> Thanks Scott!
>
> Will you please suggest best way to debug this kind of problem?
>
> Mustafa.
>
> --- On Mon, 3/1/10, Scott Cain <scott@...> wrote:
>
>> From: Scott Cain <scott@...>
>> Subject: Re: [Gmod-gbrowse] adding new glyph to library
>> To: "Syed Mustafa Hussain" <comp_sea@...>
>> Cc: "Lincoln Stein" <lincoln.stein@...>, gmod-gbrowse@...forge.net
>> Date: Monday, March 1, 2010, 9:52 PM
>> Hi Mustafa,
>>
>> The message is a debugging message that was
>> inadvertantantly left in
>> the 1.69 release, and you can ignore it, so that isn't
>> informative at
>> all.
>>
>> Sorry,
>> Scott
>>
>>
>> On Mon, Mar 1, 2010 at 11:17 AM, Syed Mustafa Hussain
>> <comp_sea@...>
>> wrote:
>> > Lincoln,
>> >
>> > Glyph.pm might not be a problem as other glyphs
>> including "allele_tower" are showing up.
>> >
>> > error_log is showing only this error:
>> >
>> > ..... Bio::Graphics::BrowserConfig=HASH(0x1c25930) at
>> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>> line 587., .....
>> >
>> > Thanks,
>> > Mustafa.
>> >
>> > --- On Sat, 2/27/10, Lincoln Stein <lincoln.stein@...>
>> wrote:
>> >
>> >> From: Lincoln Stein <lincoln.stein@...>
>> >> Subject: Re: [Gmod-gbrowse] adding new glyph to
>> library
>> >> To: "Syed Mustafa Hussain" <comp_sea@...>
>> >> Cc: gmod-gbrowse@...
>> >> Date: Saturday, February 27, 2010, 3:41 AM
>> >> You need to copy the glyph.pm file
>> >> into the appropriate library in your perl search
>> path.
>> >> Neither of these paths look right.
>> >> Lincoln
>> >>
>> >> On Fri, Feb 26, 2010 at 4:26 PM,
>> >> Syed Mustafa Hussain <comp_sea@...>
>> >> wrote:
>> >>
>> >>
>> >>
>> >> Hi,
>> >>
>> >>
>> >>
>> >> I want to add allele_column_multi glyph to glyph
>> library. I
>> >> have copied module to both bioperl
>> Bio::Graphics::Glyphs
>> >> library and lib inside
>> >> /usr/local/Generic-Genome-Browser-1.69/lib and I
>> have in
>> >> config file:
>> >>
>> >>
>> >>
>> >> [SNP:50]
>> >>
>> >> feature        = SNP
>> >>
>> >> glyph          = allele_column_multi
>> >>
>> >> alleles        = A/T
>> >>
>> >> majorcolor     = blue
>> >>
>> >> minorcolor     = red
>> >>
>> >> ref_strand     = '+'
>> >>
>> >> freq           =
>> >> 'ASW:0.3;CEU:0.6;CHB:0.4;CHD:0.5'
>> >>
>> >>
>> >>
>> >> But I do not see any image in detail panel. If I
>> substitute
>> >> allele_column_multi glyph with some other glyph it
>> is
>> >> visible.
>> >>
>> >>
>> >>
>> >> Whatelse I need to do to make it appear. What is
>> the
>> >> procedure to add new glyph.
>> >>
>> >>
>> >>
>> >> Thanks,
>> >>
>> >> Mustafa.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >>
>> >> Download Intel® Parallel Studio Eval
>> >>
>> >> Try the new software tools for yourself. Speed
>> compiling,
>> >> find bugs
>> >>
>> >> proactively, and fine-tune applications for
>> parallel
>> >> performance.
>> >>
>> >> See why Intel Parallel Studio got high marks
>> during beta.
>> >>
>> >> http://p.sf.net/sfu/intel-sw-dev
>> >>
>> >> _______________________________________________
>> >>
>> >> Gmod-gbrowse mailing list
>> >>
>> >> Gmod-gbrowse@...
>> >>
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> 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 <Renata.Musa@...>
>> >>
>> >>
>> >>
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Download Intel® Parallel Studio Eval
>> > Try the new software tools for yourself. Speed
>> compiling, find bugs
>> > proactively, and fine-tune applications for parallel
>> performance.
>> > See why Intel Parallel Studio got high marks during
>> beta.
>> > http://p.sf.net/sfu/intel-sw-dev
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > Gmod-gbrowse@...
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.
>>
>>        scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)
>>            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

------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
Jayararaman, Pushkala | 2 Mar 00:05 2010
Picon

Re: Slave rendering error - works now!

Hello,

The slave renderers seem to work now. The issue was with the

1.       Firewall settings and

2.       SELinux settings.

I “disabled” all of them and I seem to get them all working now. Even “permissive” in SELinux doesn’t seem to work.

But wouldn’t that be a compromised security issue if we disabled all of our firewalls and SELinux settings?  What would the solution be?

 

Pushkala

 

 

 

 

From: Lincoln Stein [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org]
Sent: Friday, February 26, 2010 5:44 PM
To: Jayararaman, Pushkala
Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
Subject: Re: [Gmod-gbrowse] Slave rendering error

 

Then I don't understand what's going on, unless for some reason domain name resolution isn't working properly for the web server. Perhaps try changing the slave setting in the gbrowse config file to http://127.0.0.1:8101, instead of using "localhost"

 

Lincoln

On Fri, Feb 26, 2010 at 5:46 PM, Jayararaman, Pushkala <pjayaraman-gYfhEnJJ71g@public.gmane.org> wrote:

I tried typing "test"



sudo -u apache telnet localhost 8101
Trying 127.0.0.1...
Connected to localhost.localdomain (127.0.0.1).
Escape character is '^]'.

:q


HTTP/1.1 400 Bad Request

Date: Fri, 26 Feb 2010 22:40:06 GMT


Server: libwww-perl-daemon/5.827
Content-Type: text/html
Content-Length: 57

<title>400 Bad Request</title>
<h1>400 Bad Request</h1>

Connection closed by foreign host.

Pushkala



-----Original Message-----
From: Lincoln Stein [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org]

Sent: Fri 2/26/2010 4:08 PM
To: Jayararaman, Pushkala
Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
Subject: Re: [Gmod-gbrowse] Slave rendering error

Did you try typing something to slave when you were running as apache, or
did it close the connection by itself?

Lincoln

On Fri, Feb 26, 2010 at 5:04 PM, Jayararaman, Pushkala
<pjayaraman-gYfhEnJJ71g@public.gmane.org>wrote:

>  1. Running as myself:
> su - pjayaraman
> [pjayaraman <at> localhost ~]$ telnet localhost 8101
> Trying 127.0.0.1...
> Connected to localhost.localdomain (127.0.0.1).
> Escape character is '^]'.
> test
> HTTP/1.1 400 Bad Request
> Date: Fri, 26 Feb 2010 21:43:09 GMT
> Server: libwww-perl-daemon/5.827
> Content-Type: text/html
> Content-Length: 57
>
> <title>400 Bad Request</title>
> <h1>400 Bad Request</h1>
>
> Connection closed by foreign host.
>
> 2. Running as root:
>  su - root
> Password:
> [root <at> localhost ~]# telnet localhost 8101
> Trying 127.0.0.1...
> Connected to localhost.localdomain (127.0.0.1).
> Escape character is '^]'.
> test
> HTTP/1.1 400 Bad Request
> Date: Fri, 26 Feb 2010 21:43:56 GMT
> Server: libwww-perl-daemon/5.827
> Content-Type: text/html
> Content-Length: 57
>
> <title>400 Bad Request</title>
> <h1>400 Bad Request</h1>
>
> Connection closed by foreign host.
>
>
> 3. Running as web user "apache" (Is this the right way to run as web user?
> when I did
> %su apache
> I got "this account is currently not available")
>
>  sudo -u apache telnet localhost 8101
> Trying 127.0.0.1...
> Connected to localhost.localdomain (127.0.0.1).
> Escape character is '^]'.
>
>
> Connection closed by foreign host.
>
>
> All three show me connected. In the previous email, I was referring to the
> default ports of 8101 8102 and 8103. 8010 was a typo in my mail.
>
>
>
> Pushkala
>
>
>
>
>
>
>
> -----Original Message-----

> From: Lincoln Stein [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> ]
> Sent: Fri 2/26/2010 3:17 PM
> To: Jayararaman, Pushkala
> Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> Subject: Re: [Gmod-gbrowse] Slave rendering error
>
> Hi Pushkala,
>
> The slave log suggests that the slaves are running properly, but the error
> you get from the server log says that the master cannot connect. Did you
> try
> to telnet to localhost port 8101, and if so, what did you see?
>
> Try these things:
>
>
>    1. running as yourself, do "telnet localhost 8101"
>    2. as root, do "telnet localhost 8101"
>    3. as the web user (using sudo or su) do "telnet localhost 8101"
>
>
> If number (3) fails, then you have a SeLinux-related permissions problem.
> You need to* *grant appropriate permissions to the web user to access these
> nonstandard ports.
>
> Also, I noticed that in your original posting, you referred to a slave
> running on port 8010. If this isn't a typo, there might be a mismatch in
> port numbers between the slave and the master.
>
> Lincoln
>
> On Fri, Feb 26, 2010 at 3:12 PM, Jayararaman, Pushkala
> <pjayaraman-gYfhEnJJ71g@public.gmane.org>wrote:
>
> > Is there a problem with permissions..?
> > I am working on the system as root. Would that be the problem?
> >
> > Pushkala
> >
> > -----Original Message-----
> > From: gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org

> > [mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>
> ]
> > Sent: Friday, February 26, 2010 10:13 AM
> > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > Subject: Gmod-gbrowse Digest, Vol 45, Issue 93
> >
> > Send Gmod-gbrowse mailing list submissions to
> >        gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >        https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > or, via email, send a message with subject or body 'help' to
> >        gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> >
> > You can reach the person managing the list at
> >        gmod-gbrowse-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Gmod-gbrowse digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: [Gmod-help] gbrowse_syn (Peter)
> >   2. Re: gbrowse_img+remote feature (Prem Anand)
> >   3. Re: gbrowse_img+remote feature (Lincoln Stein)
> >   4. Re: Slave rendering error (Lincoln Stein)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 26 Feb 2010 15:47:59 +0000
> > From: Peter <biopython-amNUQouXnSY2epGFuHBODCp2UmYkHbXO@public.gmane.org>
> > Subject: Re: [Gmod-gbrowse] [Gmod-help] gbrowse_syn
> > To: Michael Paulini <mh6-5fLPn3lgkryFxr2TtlUqVg@public.gmane.org>
> > Cc: Chris Fields <cjfields-nzINlOoChub2fBVCVOL8/A@public.gmane.org>, mckays-FePsPjn27tw@public.gmane.org,
> >         gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > Message-ID:
> >         <320fb6e01002260747o61f2f667taa57d10917eda9a8-JsoAwUIsXov6gbPvEgmw2w@public.gmane.org.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Fri, Feb 26, 2010 at 3:31 PM, Michael Paulini <mh6-5fLPn3lgkryFxr2TtlUqVg@public.gmane.org>
> > wrote:
> > >
> > > Yup, I do:
> >
> > Thanks - it turns out I had seen it before after all, my mistake:
> > http://lists.open-bio.org/pipermail/open-bio-l/2010-February/000615.html
> >
> > Peter
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 26 Feb 2010 16:05:11 +0000
> > From: Prem Anand <prem.apa-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > Subject: Re: [Gmod-gbrowse] gbrowse_img+remote feature
> > To: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > Message-ID:
> >         <a38704bf1002260805g6ba6606cvd27036107156631a-JsoAwUIsXov6gbPvEgmw2w@public.gmane.org.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi Lincoln
> >
> > We use 1.70.  Yes when GBrowse is generating the image link, it do
> > append a
> > session id, and could see the remote das tracks when the image link is
> > pasted directly.
> >
> > But I am trying to generate the gbrowse_img url through my cgi code and
> > trying to embed it on the page, not going through gbrowse, as I need to
> > display a static image, along with some other results.  In this case,
> > the
> > remote das track is not getting displayed.  Infact both(local and
> > remote)
> > databases are in the same server, but we wanted to split the databases
> > for
> > easy maintenance.
> >
> > This show the remote das track:
> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
> > TRACK;width=800;id=836eafe0a66378536ffb40786a1b561f;keystyle=between;gri
> > d=on;embed=1
> >
> >
> > Doesn't show:
> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
> > TRACK;width=800;keystyle=between;grid=on;embed=1
> >
> >
> > And if both the tracks are local(in the same conf file/single database),
> > then there is no problem. Both tracks are visible with gbrowse_img call
> > even
> > without session id.
> >
> > I tried gbgff approach as well, but have other issues with that like
> > feature->display_name not getting displayed for remote track, so
> > sticking to
> > das approach for now.
> >
> > Many Thanks for your time,
> > Prem
> >
> >
> >
> > On Fri, Feb 26, 2010 at 3:23 PM, Lincoln Stein
> > <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>wrote:
> >
> > > Hi Prem,
> > >
> > > Which version of GBrowse are you seeing this behavior in? You do
> > indeed
> > > need to append a session ID to the gbrowse_img URL, but gbrowse is
> > supposed
> > > to do this for you when it generates the "image" link.
> > >
> > > Lincoln
> > >
> > >
> > > On Thu, Feb 25, 2010 at 1:21 PM, Premanand Achuthan <
> > > Premanand.Achuthan-piTOwl1TIVXQzY9nttDBhA@public.gmane.org> wrote:
> > >
> > >> Hi All
> > >>
> > >> I have a track that calls a remote feature through das.  The remote
> > >> track along with other tracks is displayed properly when the call is
> > >> made through /cgi-bin/gbrowse/.
> > >> But the remote track alone is not shown (other tracks are shown) if I
> > >> wanted to generate the gbrowse image via /cgi-bin/gbrowse_img call.
> > >>
> > >> Upon examing the gbrowse sessions file, the page_settings is empty
> > >> $D = {'.source' => '01_Hs_NCBI36','01_Hs_NCBI36' => {'page_settings'
> > =>
> > >> {},'plugins'=>........;$D
> > >> compared to the previous call (cgi-bin/gbrowse)
> > >>
> > >> I am able to see the track, if the session id(generated by the first
> > >> call) is appended to the url, like
> > >>
> > >>
> > /cgi-bin/gbrowse_img/dsn/?name=chr11:2110344..2139147;type=bla+bla+bla;i
> > d=0fd35a9527c74e5da0d96d4d8aa0651e;other_img_params
> > >>
> > >> How to get the proper page_settings in the gbrowse session file for
> > >> remote tracks?
> > >>
> > >> Am I missing something? or doing something wrong?
> > >>
> > >> Thanks to Everyone,
> > >> Prem
> > >>
> > >>
> > >>
> > ------------------------------------------------------------------------
> > ------
> > >> Download Intel® Parallel Studio Eval
>
> > >> Try the new software tools for yourself. Speed compiling, find bugs
> > >> proactively, and fine-tune applications for parallel performance.
> > >> See why Intel Parallel Studio got high marks during beta.
> > >> http://p.sf.net/sfu/intel-sw-dev
> > >> _______________________________________________
> > >> Gmod-gbrowse mailing list
> > >> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >>
> > >
> > >
> > >
> > > --
> > > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > ------
> > > Download Intel® Parallel Studio Eval
>
> > > Try the new software tools for yourself. Speed compiling, find bugs
> > > proactively, and fine-tune applications for parallel performance.
> > > See why Intel Parallel Studio got high marks during beta.
> > > http://p.sf.net/sfu/intel-sw-dev
> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 26 Feb 2010 11:11:02 -0500
> > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > Subject: Re: [Gmod-gbrowse] gbrowse_img+remote feature
> > To: Prem Anand <prem.apa-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > Message-ID:
> >         <6dce9a0b1002260811h1135ab99ga82c812a7bfb06e-JsoAwUIsXotQFR93xxRIaA@public.gmane.orgcom>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > How is the remote track added? Is it added by uploading the URL, or
> > using
> > the "remote feature" option in the config file. In the latter case, it
> > should not be necessary to include the session ID.
> >
> > Lincoln
> >
> > On Fri, Feb 26, 2010 at 11:05 AM, Prem Anand <prem.apa-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
> >
> > > Hi Lincoln
> > >
> > > We use 1.70.  Yes when GBrowse is generating the image link, it do
> > append a
> > > session id, and could see the remote das tracks when the image link is
> > > pasted directly.
> > >
> > > But I am trying to generate the gbrowse_img url through my cgi code
> > and
> > > trying to embed it on the page, not going through gbrowse, as I need
> > to
> > > display a static image, along with some other results.  In this case,
> > the
> > > remote das track is not getting displayed.  Infact both(local and
> > remote)
> > > databases are in the same server, but we wanted to split the databases
> > for
> > > easy maintenance.
> > >
> > > This show the remote das track:
> > >
> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
> > TRACK;width=800;id=836eafe0a66378536ffb40786a1b561f;keystyle=between;gri
> > d=on;embed=1
> > >
> > >
> > > Doesn't show:
> > >
> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
> > TRACK;width=800;keystyle=between;grid=on;embed=1
> > >
> > >
> > > And if both the tracks are local(in the same conf file/single
> > database),
> > > then there is no problem. Both tracks are visible with gbrowse_img
> > call even
> > > without session id.
> > >
> > > I tried gbgff approach as well, but have other issues with that like
> > > feature->display_name not getting displayed for remote track, so
> > sticking to
> > > das approach for now.
> > >
> > > Many Thanks for your time,
> > > Prem
> > >
> > >
> > >
> > > On Fri, Feb 26, 2010 at 3:23 PM, Lincoln Stein
> > <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>wrote:
> > >
> > >> Hi Prem,
> > >>
> > >> Which version of GBrowse are you seeing this behavior in? You do
> > indeed
> > >> need to append a session ID to the gbrowse_img URL, but gbrowse is
> > supposed
> > >> to do this for you when it generates the "image" link.
> > >>
> > >> Lincoln
> > >>
> > >>
> > >> On Thu, Feb 25, 2010 at 1:21 PM, Premanand Achuthan <
> > >> Premanand.Achuthan-piTOwl1TIVXQzY9nttDBhA@public.gmane.org> wrote:
> > >>
> > >>> Hi All
> > >>>
> > >>> I have a track that calls a remote feature through das.  The remote
> > >>> track along with other tracks is displayed properly when the call is
> > >>> made through /cgi-bin/gbrowse/.
> > >>> But the remote track alone is not shown (other tracks are shown) if
> > I
> > >>> wanted to generate the gbrowse image via /cgi-bin/gbrowse_img call.
> > >>>
> > >>> Upon examing the gbrowse sessions file, the page_settings is empty
> > >>> $D = {'.source' => '01_Hs_NCBI36','01_Hs_NCBI36' => {'page_settings'
> > =>
> > >>> {},'plugins'=>........;$D
> > >>> compared to the previous call (cgi-bin/gbrowse)
> > >>>
> > >>> I am able to see the track, if the session id(generated by the first
> > >>> call) is appended to the url, like
> > >>>
> > >>>
> > /cgi-bin/gbrowse_img/dsn/?name=chr11:2110344..2139147;type=bla+bla+bla;i
> > d=0fd35a9527c74e5da0d96d4d8aa0651e;other_img_params
> > >>>
> > >>> How to get the proper page_settings in the gbrowse session file for
> > >>> remote tracks?
> > >>>
> > >>> Am I missing something? or doing something wrong?
> > >>>
> > >>> Thanks to Everyone,
> > >>> Prem
> > >>>
> > >>>
> > >>>
> > ------------------------------------------------------------------------
> > ------
> > >>> Download Intel® Parallel Studio Eval
>
> > >>> Try the new software tools for yourself. Speed compiling, find bugs
> > >>> proactively, and fine-tune applications for parallel performance.
> > >>> See why Intel Parallel Studio got high marks during beta.
> > >>> http://p.sf.net/sfu/intel-sw-dev
> > >>> _______________________________________________
> > >>> Gmod-gbrowse mailing list
> > >>> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >>>
> > >>
> > >>
> > >>
> > >> --
> > >> 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
> > >>
> > >>
> > >>
> > ------------------------------------------------------------------------
> > ------
> > >> Download Intel® Parallel Studio Eval
>
> > >> Try the new software tools for yourself. Speed compiling, find bugs
> > >> proactively, and fine-tune applications for parallel performance.
> > >> See why Intel Parallel Studio got high marks during beta.
> > >> http://p.sf.net/sfu/intel-sw-dev
> > >> _______________________________________________
> > >> Gmod-gbrowse mailing list
> > >> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >>
> > >>
> > >
> >
> >
> > --
> > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Fri, 26 Feb 2010 11:12:36 -0500
> > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > Subject: Re: [Gmod-gbrowse] Slave rendering error
> > To: "Jayararaman, Pushkala" <pjayaraman-gYfhEnJJ71g@public.gmane.org>
> > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > Message-ID:
> >         <6dce9a0b1002260812te864bf0i647e08360181b422-JsoAwUIsXotQFR93xxRIaA@public.gmane.orgcom>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi,
> >
> > I am interested in the contents of the gbrowse_slave error log, which is
> > a
> > separate error log usually written to /var/log/gbrowse/gbrowse_slave.
> > The
> > apache error log is only showing that the slave cannot be reached.
> >
> > Lincoln
> >
> > On Thu, Feb 25, 2010 at 4:20 PM, Jayararaman, Pushkala
> > <pjayaraman-gYfhEnJJ71g@public.gmane.org>wrote:
> >
> > >  here is the error logs from apache:
> > >
> > >
> > > [Thu Feb 25 15:13:02 2010] [error] [client 127.0.0.1] GBROWSE NOTICE:
> > To
> > > enable PDF generation, please enter the directory "/var/www" and run
> > the
> > > commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache
> > .inkscape
> > > .gnome2".  To turn off this message add "generate pdf = 0" to the
> > [GENERAL]
> > > section of your GBrowse.conf configuration file., referer:
> > > http://localhost/gb2/gbrowse/volvox/?source=volvox
> > >
> > r/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/
> > Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > Transp TranslationF with http://127.0.0.1:8103 at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > TranslationR Genes Translation LTRs tRNAs with http://127.0.0.1:8101
> > at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > TranslationR Genes Translation LTRs tRNAs with http://127.0.0.1:8103
> > at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > DNA/GC Content ncRNA CDS with http://127.0.0.1:8101 at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > DNA/GC Content ncRNA CDS with http://127.0.0.1:8102 at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:07 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > GC:region with http://127.0.0.1:8102 at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:07 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > GC:region with http://127.0.0.1:8103 at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > > [Thu Feb 25 15:13:07 2010] [error] [client 127.0.0.1] retrying fetch
> > of
> > > Centro:overview with http://127.0.0.1:8102 at
> > >
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
> > cs/Browser2/RenderPanels.pm
> > > line 690., referer:
> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
> > >
> > >
> > > There seems to be a problem in the RenderPanels.pm
> > > The error logs have been consistently pointing to that. How do I work
> > > around this?
> > >
> > >
> > > Pushkala
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org [
> > >

> > mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org<gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org>
> <gmod-gbrowse-request <at> l
> > ists.sourceforge.net>
> > > ]
> > > Sent: Thu 2/25/2010 3:14 PM
> > > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > Subject: Gmod-gbrowse Digest, Vol 45, Issue 86
> > >
> > > Send Gmod-gbrowse mailing list submissions to
> > >         gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > >         https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > or, via email, send a message with subject or body 'help' to
> > >         gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > >
> > > You can reach the person managing the list at
> > >         gmod-gbrowse-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of Gmod-gbrowse digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. gbrowse2 search bug? (Christopher Porter)
> > >    2. Re: gbrowse2 search bug? (Lincoln Stein)
> > >    3. (no subject) (Syed Mustafa Hussain)
> > >    4. loader for GFF3 (Syed Mustafa Hussain)
> > >    5. Re: gbrowse2 search bug? (Lincoln Stein)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Thu, 25 Feb 2010 15:20:33 -0500
> > > From: Christopher Porter <cporter-V3tf7a8Vaus@public.gmane.org>
> > > Subject: [Gmod-gbrowse] gbrowse2 search bug?
> > > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > Message-ID: <7B1B25A5-A956-4355-A455-B283154462DF-V3tf7a8Vaus@public.gmane.org>
> > > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> > >
> > >
> > > Gbrowse 2.0 is returning an error when I search for a chromosomal
> > > region under a specific set of circumstances - is this a known
> > > problem, or is there a configuration option I can change to make this
> > > go away?
> > >
> > > To reproduce the error:
> > >
> > > 1) Search for a gene using a partial gene symbol (e.g. Pou) which will
> > > return a list of genes matching the name (autocomplete on).
> > > 2) Select one of the returned genes by clicking on the gene symbol.
> > >
> > > After doing this, any subsequent search by location will return the
> > > error "The landmark named chr1:167805616..167865031 is not recognized.
> > > See the help pages for suggestions". This happens both for searches
> > > using the 'landmark or region' search field, or using a ?
> > > name=<location> URL. As far as I can tell, this can only be resolved
> > > by hitting the 'Reset' link, after which location searches work again.
> > >
> > > Selecting the location link at step (2) doesn't result in the error-
> > > prone state being set.
> > >
> > > Running gbrowse2 (2.0) with mysql backend plus BAM flatfiles; scaffold
> > > is mouse genomic sequence.
> > >
> > > Any suggestions?
> > >
> > > Thanks,
> > >
> > > Chris
> > >
> > >
> > > --------------------
> > > Confidentiality Statement - The contents of this e-mail, including its
> > > attachment, are intended for the exclusive use of the recipient and
> > may
> > > contain confidential or privileged information.  If you are not the
> > intended
> > > recipient, you are strictly prohibited from reading, using,
> > disclosing,
> > > copying, or distributing this e-mail or any of its contents.  If you
> > > received this e-mail in error, please notify the sender by reply
> > e-mail
> > > immediately or the Privacy Office (privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK@public.gmane.org ) and
> > > permanently delete this e-mail and its attachments, along with any
> > copies
> > > thereof.  Thank you.
> > >
> > > Avis de confidentialit? - Ce courriel, y compris ses pi?ces jointes,
> > > s'adresse au destinataire uniquement et pourrait contenir des
> > renseignements
> > > confidentiels. Si vous n'?tes pas le bon destinataire, il est
> > strictement
> > > interdit de lire, d'utiliser, de divulguer, de copier ou de diffuser
> > ce
> > > courriel ou son contenu, en partie ou en entier. Si vous avez re?u ce
> > > courriel par erreur, veuillez en informer imm?diatement l'exp?diteur
> > ou le
> > > bureau de la Protection des renseignements personnels (
> > > info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys@public.gmane.org), puis effacez le courriel ainsi que
> > les
> > > pi?ces jointes et toute autre copie. Merci.
> > > --------------------
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Thu, 25 Feb 2010 16:04:27 -0500
> > > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > > Subject: Re: [Gmod-gbrowse] gbrowse2 search bug?
> > > To: Christopher Porter <cporter-V3tf7a8Vaus@public.gmane.org>
> > > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > Message-ID:
> > >         <6dce9a0b1002251304g11805485g5d604012a6cddac1-JsoAwUIsXov6gbPvEgmw2w@public.gmane.org.com>
> > > Content-Type: text/plain; charset="windows-1252"
> > >
> > > This is a known problem and I am working on it.
> > >
> > > Lincoln
> > >
> > > On Thu, Feb 25, 2010 at 3:20 PM, Christopher Porter <cporter-V3tf7a8Vaus@public.gmane.org>
> > > wrote:
> > >
> > > >
> > > > Gbrowse 2.0 is returning an error when I search for a chromosomal
> > region
> > > > under a specific set of circumstances - is this a known problem, or
> > is
> > > there
> > > > a configuration option I can change to make this go away?
> > > >
> > > > To reproduce the error:
> > > >
> > > > 1) Search for a gene using a partial gene symbol (e.g. Pou) which
> > will
> > > > return a list of genes matching the name (autocomplete on).
> > > > 2) Select one of the returned genes by clicking on the gene symbol.
> > > >
> > > > After doing this, any subsequent search by location will return the
> > error
> > > > "The landmark named chr1:167805616..167865031 is not recognized. See
> > the
> > > > help pages for suggestions". This happens both for searches using
> > the
> > > > 'landmark or region' search field, or using a ?name=<location> URL.
> > As
> > > far
> > > > as I can tell, this can only be resolved by hitting the 'Reset'
> > link,
> > > after
> > > > which location searches work again.
> > > >
> > > > Selecting the location link at step (2) doesn't result in the
> > error-prone
> > > > state being set.
> > > >
> > > > Running gbrowse2 (2.0) with mysql backend plus BAM flatfiles;
> > scaffold is
> > > > mouse genomic sequence.
> > > >
> > > > Any suggestions?
> > > >
> > > > Thanks,
> > > >
> > > > Chris
> > > >
> > > >
> > > > --------------------
> > > > Confidentiality Statement - The contents of this e-mail, including
> > its
> > > > attachment, are intended for the exclusive use of the recipient and
> > may
> > > > contain confidential or privileged information.  If you are not the
> > > intended
> > > > recipient, you are strictly prohibited from reading, using,
> > disclosing,
> > > > copying, or distributing this e-mail or any of its contents.  If you
> > > > received this e-mail in error, please notify the sender by reply
> > e-mail
> > > > immediately or the Privacy Office (privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK@public.gmane.org )
> > and
> > > > permanently delete this e-mail and its attachments, along with any
> > copies
> > > > thereof.  Thank you.
> > > >
> > > > Avis de confidentialit? ? Ce courriel, y compris ses pi?ces jointes,
> > > > s?adresse au destinataire uniquement et pourrait contenir des
> > > renseignements
> > > > confidentiels. Si vous n??tes pas le bon destinataire, il est
> > strictement
> > > > interdit de lire, d?utiliser, de divulguer, de copier ou de diffuser
> > ce
> > > > courriel ou son contenu, en partie ou en entier. Si vous avez re?u
> > ce
> > > > courriel par erreur, veuillez en informer imm?diatement l?exp?diteur
> > ou
> > > le
> > > > bureau de la Protection des renseignements personnels (
> > > > info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys@public.gmane.org), puis effacez le courriel ainsi que
> > les
> > > > pi?ces jointes et toute autre copie. Merci.
> > > > --------------------
> > > >
> > > >
> > > >
> > > >
> > >
> > ------------------------------------------------------------------------
> > ------
> > > > Download Intel? Parallel Studio Eval
> > > > Try the new software tools for yourself. Speed compiling, find bugs
> > > > proactively, and fine-tune applications for parallel performance.
> > > > See why Intel Parallel Studio got high marks during beta.
> > > > http://p.sf.net/sfu/intel-sw-dev
> > > > _______________________________________________
> > > > Gmod-gbrowse mailing list
> > > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > >
> > > >
> > >
> > >
> > > --
> > > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Thu, 25 Feb 2010 13:07:13 -0800 (PST)
> > > From: Syed Mustafa Hussain <comp_sea-/E1597aS9LQAvxtiuMwx3w@public.gmane.org>
> > > Subject: [Gmod-gbrowse] (no subject)
> > > To: Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > Message-ID: <141654.38826.qm-XCd8ux6whGmvuULXzWHTWIglqE1Y4D90QQ4Iyu8u01E@public.gmane.org>
> > > Content-Type: text/plain; charset=us-ascii
> > >
> > > Hi,
> > >
> > > Does someone knows a loader which is faster than
> > bp_seqfeature_load.PLS and
> > > create database for Bio::DB::SeqFeature::Store adaptor. I have nearly
> > 100GB
> > > SNP data to load and currently I am using bp_seqfeature_load.PLS which
> > is
> > > kind of slow. I cannot use bulk_load_gff.PLS/fast_load_gff.PLS because
> > it
> > > create database for Bio::DB::GFF adaptor, for which using aggregators
> > are
> > > not convenient.
> > >
> > > Or, is there a way to tweak bulk_load_gff.PLS/fast_load_gff.PLS to
> > create
> > > database for Bio::DB::SeqFeature::Store adaptor.
> > >
> > > Thanks,
> > > Mustafa.
> > >
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Thu, 25 Feb 2010 12:42:25 -0800 (PST)
> > > From: Syed Mustafa Hussain <comp_sea-/E1597aS9LQAvxtiuMwx3w@public.gmane.org>
> > > Subject: [Gmod-gbrowse] loader for GFF3
> > > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > Message-ID: <728670.61633.qm-FlipYfUoLlOvuULXzWHTWIglqE1Y4D90QQ4Iyu8u01E@public.gmane.org>
> > > Content-Type: text/plain; charset="us-ascii"
> > >
> > > Hi,
> > >
> > > Does someone knows a loader which is faster than
> > bp_seqfeature_load.PLS and
> > > create database for Bio::DB::SeqFeature::Store adaptor. I have nearly
> > 100GB
> > > SNP data to load and currently I am using bp_seqfeature_load.PLS which
> > is
> > > kind of slow. I cannot use bulk_load_gff.PLS/fast_load_gff.PLS because
> > it
> > > create database for Bio::DB::GFF adaptor, for which using aggregators
> > are
> > > not convenient.
> > >
> > > Or, is there a way to tweak bulk_load_gff.PLS/fast_load_gff.PLS to
> > create
> > > database for Bio::DB::SeqFeature::Store adaptor.
> > >
> > > Thanks,
> > > Mustafa.
> > >
> > >
> > >
> > >
> > >
> > >
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > >
> > > ------------------------------
> > >
> > > Message: 5
> > > Date: Thu, 25 Feb 2010 16:14:43 -0500
> > > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> > > Subject: Re: [Gmod-gbrowse] gbrowse2 search bug?
> > > To: Christopher Porter <cporter-V3tf7a8Vaus@public.gmane.org>
> > > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > Message-ID:
> > >         <6dce9a0b1002251314h72810ae6ua93a50719de2b7dd-JsoAwUIsXov6gbPvEgmw2w@public.gmane.org.com>
> > > Content-Type: text/plain; charset="windows-1252"
> > >
> > > Hi Chris,
> > >
> > > Could you see what happens when you set the BAM databases search
> > options to
> > > "none"?
> > >
> > > Lincoln
> > >
> > > On Thu, Feb 25, 2010 at 3:20 PM, Christopher Porter <cporter-V3tf7a8Vaus@public.gmane.org>
> > > wrote:
> > >
> > > >
> > > > Gbrowse 2.0 is returning an error when I search for a chromosomal
> > region
> > > > under a specific set of circumstances - is this a known problem, or
> > is
> > > there
> > > > a configuration option I can change to make this go away?
> > > >
> > > > To reproduce the error:
> > > >
> > > > 1) Search for a gene using a partial gene symbol (e.g. Pou) which
> > will
> > > > return a list of genes matching the name (autocomplete on).
> > > > 2) Select one of the returned genes by clicking on the gene symbol.
> > > >
> > > > After doing this, any subsequent search by location will return the
> > error
> > > > "The landmark named chr1:167805616..167865031 is not recognized. See
> > the
> > > > help pages for suggestions". This happens both for searches using
> > the
> > > > 'landmark or region' search field, or using a ?name=<location> URL.
> > As
> > > far
> > > > as I can tell, this can only be resolved by hitting the 'Reset'
> > link,
> > > after
> > > > which location searches work again.
> > > >
> > > > Selecting the location link at step (2) doesn't result in the
> > error-prone
> > > > state being set.
> > > >
> > > > Running gbrowse2 (2.0) with mysql backend plus BAM flatfiles;
> > scaffold is
> > > > mouse genomic sequence.
> > > >
> > > > Any suggestions?
> > > >
> > > > Thanks,
> > > >
> > > > Chris
> > > >
> > > >
> > > > --------------------
> > > > Confidentiality Statement - The contents of this e-mail, including
> > its
> > > > attachment, are intended for the exclusive use of the recipient and
> > may
> > > > contain confidential or privileged information.  If you are not the
> > > intended
> > > > recipient, you are strictly prohibited from reading, using,
> > disclosing,
> > > > copying, or distributing this e-mail or any of its contents.  If you
> > > > received this e-mail in error, please notify the sender by reply
> > e-mail
> > > > immediately or the Privacy Office (privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK@public.gmane.org )
> > and
> > > > permanently delete this e-mail and its attachments, along with any
> > copies
> > > > thereof.  Thank you.
> > > >
> > > > Avis de confidentialit? ? Ce courriel, y compris ses pi?ces jointes,
> > > > s?adresse au destinataire uniquement et pourrait contenir des
> > > renseignements
> > > > confidentiels. Si vous n??tes pas le bon destinataire, il est
> > strictement
> > > > interdit de lire, d?utiliser, de divulguer, de copier ou de diffuser
> > ce
> > > > courriel ou son contenu, en partie ou en entier. Si vous avez re?u
> > ce
> > > > courriel par erreur, veuillez en informer imm?diatement l?exp?diteur
> > ou
> > > le
> > > > bureau de la Protection des renseignements personnels (
> > > > info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys@public.gmane.org), puis effacez le courriel ainsi que
> > les
> > > > pi?ces jointes et toute autre copie. Merci.
> > > > --------------------
> > > >
> > > >
> > > >
> > > >
> > >
> > ------------------------------------------------------------------------
> > ------
> > > > Download Intel? Parallel Studio Eval
> > > > Try the new software tools for yourself. Speed compiling, find bugs
> > > > proactively, and fine-tune applications for parallel performance.
> > > > See why Intel Parallel Studio got high marks during beta.
> > > > http://p.sf.net/sfu/intel-sw-dev
> > > > _______________________________________________
> > > > Gmod-gbrowse mailing list
> > > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > >
> > > >
> > >
> > >
> > > --
> > > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > >
> > > ------------------------------
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > ------
> > > Download Intel? Parallel Studio Eval
> > > Try the new software tools for yourself. Speed compiling, find bugs
> > > proactively, and fine-tune applications for parallel performance.
> > > See why Intel Parallel Studio got high marks during beta.
> > > http://p.sf.net/sfu/intel-sw-dev
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> > >
> > > End of Gmod-gbrowse Digest, Vol 45, Issue 86
> > > ********************************************
> > >
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > ------
> > > Download Intel® Parallel Studio Eval
>
> > > Try the new software tools for yourself. Speed compiling, find bugs
> > > proactively, and fine-tune applications for parallel performance.
> > > See why Intel Parallel Studio got high marks during beta.
> > > http://p.sf.net/sfu/intel-sw-dev
> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> > >
> >
> >
> > --
> > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> > ------------------------------------------------------------------------
> > ------
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed compiling, find bugs
> > proactively, and fine-tune applications for parallel performance.
> > See why Intel Parallel Studio got high marks during beta.
> > http://p.sf.net/sfu/intel-sw-dev
> >
> > ------------------------------
> >
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> >
> > End of Gmod-gbrowse Digest, Vol 45, Issue 93
> > ********************************************
> >
> >
> >
> ------------------------------------------------------------------------------
>
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed compiling, find bugs
> > proactively, and fine-tune applications for parallel performance.
> > See why Intel Parallel Studio got high marks during beta.
> > http://p.sf.net/sfu/intel-sw-dev
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
>
>
>
> --
> 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
>
>


--
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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>




--
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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>

------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
CHAN, KENNETH 1 [AG/7721] | 2 Mar 13:28 2010
Picon

questions about sequence strand orientation and problem in show_mismatch

Hello all,
  I have been struggling with displaying the sequences correctly for
different strands combination. I created 4 testing sequences with the
following variation:
1. strand (+); 'Target start' < 'Target end'; 'Target strand' (+)
2. -; >; -
3. -; <; +
4. +; >; -
By deliberately creating some artificial sequences, I was expecting all
4 will display the same sequence as the refSeq with no mismatch.
However, besides Case 1, the other 3 cases could not get what I was
expecting. (the seqFAST-3.fa and testing-3.gff3 files are attached, its
screenshot is in testing-3.png). I couldn't find much information on how
gbrowse actually handles the combination of this 3 information (strand,
target position and target strand). 
  Doing this test leads to my second question. As seen in testing-3.png,
the 3rd sequence (seqPNN) is the same as the reference Seq (refSeq)
however it is shown as mismatch (red represents mismatch). Why is it?
And what are the criteria for determining the mismatches?
  I also tried using a longer reference sequence. Somehow, some bases in
seqPNN changed the color as in test-3-200.png. (The attached
testing-3-200.gff3 and seqFASTA-3-200.fa are for obtaining this result)
It doesn't seem right, does it?
  Finally, I tried applying the canonical_strand attribute but didn't
see any changes for turning it on or off. Did I do something wrong?
  The following shows the track configuration I applied:

[testStrandDir]
feature = featureType
glyph = segments
height = 12
draw_target = 1
strand_arrow = 1
show_mismatch = 1
mismatch_color = red
canonical_strand = 1
label = 1
bgcolor = green
key = testing Strand Direction

PS: I tried to make sure the testing was not affected by the cached
files so I deleted the directory.index and the corresponding tmp folder
in gbrowse/tmp before refreshing the web page each time. 

  Thanks for your time.

Regards,
Kenneth

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Attachment (seqFASTA-3.fa): application/octet-stream, 134 bytes
Attachment (testing-3.gff3): application/octet-stream, 548 bytes
Attachment (testing-3-200.gff3): application/octet-stream, 552 bytes
Attachment (seqFASTA-3-200.fa): application/octet-stream, 442 bytes
------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Josh Goodman | 2 Mar 15:58 2010
Picon

Re: Slave rendering error - works now!

Hi Pushkala,

Yes you are definitely at risk, especially if you are on a public network.

The SELinux permissive mode only logs enforcement actions, it does not do any enforcement
whatsoever.  If you enable permissive mode with your firewall disabled and your slave quits working,
I would strongly suspect that you have a filesystem labeling problem.  To resolve this run these
commands as root.

# touch /.autorelabel
# reboot

See http://wiki.centos.org/HowTos/SELinux for more tips including how to allow non standard apache
ports.

For your firewall you will need to configure rules that are specific to your situation.  The CentOS
HowTo on IPTables (http://wiki.centos.org/HowTos/Network/IPTables) gives you enough information to
allow you to add some simple rules to your firewall that should allow the slaves to accept connections.

I would start with a simple rule test it, restrict it further, test again, etc...

e.g.
Open port 8101
# iptables -A INPUT -p tcp --dport 8101 -j ACCEPT

test gbrowse

Remove previous rule and restrict further
# iptables -D INPUT -p tcp --dport 8101 -j ACCEPT
# iptables -A INPUT -p tcp -s 192.168.0.0/24 --dport 8101 -j ACCEPT
....

Then when you are satisfied do

# /sbin/service iptables save

to save your new rule to /etc/sysconfig/iptables.

Cheers,
Josh

On 03/01/2010 06:05 PM, Jayararaman, Pushkala wrote:
> Hello,
> 
> The slave renderers seem to work now. The issue was with the
> 
> 1.       Firewall settings and
> 
> 2.       SELinux settings.
> 
> I “disabled” all of them and I seem to get them all working now. Even
> “permissive” in SELinux doesn’t seem to work.
> 
> But wouldn’t that be a compromised security issue if we disabled all of
> our firewalls and SELinux settings?  What would the solution be?
> 
>  
> 
> Pushkala
> 
>  
> 
>  
> 
>  
> 
>  
> 
> *From:* Lincoln Stein [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org]
> *Sent:* Friday, February 26, 2010 5:44 PM
> *To:* Jayararaman, Pushkala
> *Cc:* gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> *Subject:* Re: [Gmod-gbrowse] Slave rendering error
> 
>  
> 
> Then I don't understand what's going on, unless for some reason domain
> name resolution isn't working properly for the web server. Perhaps try
> changing the slave setting in the gbrowse config file to
> http://127.0.0.1:8101, instead of using "localhost"
> 
>  
> 
> Lincoln
> 
> On Fri, Feb 26, 2010 at 5:46 PM, Jayararaman, Pushkala
> <pjayaraman-gYfhEnJJ71g <at> public.gmane.org <mailto:pjayaraman-gYfhEnJJ71g <at> public.gmane.org>> wrote:
> 
> I tried typing "test"
> 
> 
> 
> sudo -u apache telnet localhost 8101
> Trying 127.0.0.1...
> Connected to localhost.localdomain (127.0.0.1).
> Escape character is '^]'.
> 
> :q
> 
> 
> HTTP/1.1 400 Bad Request
> 
> Date: Fri, 26 Feb 2010 22:40:06 GMT
> 
> 
> Server: libwww-perl-daemon/5.827
> Content-Type: text/html
> Content-Length: 57
> 
> <title>400 Bad Request</title>
> <h1>400 Bad Request</h1>
> 
> Connection closed by foreign host.
> 
> Pushkala
> 
> 
> 
> -----Original Message-----
> From: Lincoln Stein [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org]
> 
> Sent: Fri 2/26/2010 4:08 PM
> To: Jayararaman, Pushkala
> Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
> Subject: Re: [Gmod-gbrowse] Slave rendering error
> 
> Did you try typing something to slave when you were running as apache, or
> did it close the connection by itself?
> 
> Lincoln
> 
> On Fri, Feb 26, 2010 at 5:04 PM, Jayararaman, Pushkala
> <pjayaraman-gYfhEnJJ71g <at> public.gmane.org <mailto:pjayaraman-gYfhEnJJ71g <at> public.gmane.org>>wrote:
> 
>>  1. Running as myself:
>> su - pjayaraman
>> [pjayaraman <at> localhost ~]$ telnet localhost 8101
>> Trying 127.0.0.1...
>> Connected to localhost.localdomain (127.0.0.1).
>> Escape character is '^]'.
>> test
>> HTTP/1.1 400 Bad Request
>> Date: Fri, 26 Feb 2010 21:43:09 GMT
>> Server: libwww-perl-daemon/5.827
>> Content-Type: text/html
>> Content-Length: 57
>>
>> <title>400 Bad Request</title>
>> <h1>400 Bad Request</h1>
>>
>> Connection closed by foreign host.
>>
>> 2. Running as root:
>>  su - root
>> Password:
>> [root <at> localhost ~]# telnet localhost 8101
>> Trying 127.0.0.1...
>> Connected to localhost.localdomain (127.0.0.1).
>> Escape character is '^]'.
>> test
>> HTTP/1.1 400 Bad Request
>> Date: Fri, 26 Feb 2010 21:43:56 GMT
>> Server: libwww-perl-daemon/5.827
>> Content-Type: text/html
>> Content-Length: 57
>>
>> <title>400 Bad Request</title>
>> <h1>400 Bad Request</h1>
>>
>> Connection closed by foreign host.
>>
>>
>> 3. Running as web user "apache" (Is this the right way to run as web user?
>> when I did
>> %su apache
>> I got "this account is currently not available")
>>
>>  sudo -u apache telnet localhost 8101
>> Trying 127.0.0.1...
>> Connected to localhost.localdomain (127.0.0.1).
>> Escape character is '^]'.
>>
>>
>> Connection closed by foreign host.
>>
>>
>> All three show me connected. In the previous email, I was referring to the
>> default ports of 8101 8102 and 8103. 8010 was a typo in my mail.
>>
>>
>>
>> Pushkala
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
> 
>> From: Lincoln Stein
> [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org<lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> ]
>> Sent: Fri 2/26/2010 3:17 PM
>> To: Jayararaman, Pushkala
>> Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> Subject: Re: [Gmod-gbrowse] Slave rendering error
>>
>> Hi Pushkala,
>>
>> The slave log suggests that the slaves are running properly, but the error
>> you get from the server log says that the master cannot connect. Did you
>> try
>> to telnet to localhost port 8101, and if so, what did you see?
>>
>> Try these things:
>>
>>
>>    1. running as yourself, do "telnet localhost 8101"
>>    2. as root, do "telnet localhost 8101"
>>    3. as the web user (using sudo or su) do "telnet localhost 8101"
>>
>>
>> If number (3) fails, then you have a SeLinux-related permissions problem.
>> You need to* *grant appropriate permissions to the web user to access these
>> nonstandard ports.
>>
>> Also, I noticed that in your original posting, you referred to a slave
>> running on port 8010. If this isn't a typo, there might be a mismatch in
>> port numbers between the slave and the master.
>>
>> Lincoln
>>
>> On Fri, Feb 26, 2010 at 3:12 PM, Jayararaman, Pushkala
>> <pjayaraman-gYfhEnJJ71g <at> public.gmane.org <mailto:pjayaraman-gYfhEnJJ71g <at> public.gmane.org>>wrote:
>>
>> > Is there a problem with permissions..?
>> > I am working on the system as root. Would that be the problem?
>> >
>> > Pushkala
>> >
>> > -----Original Message-----
>> > From: gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
> 
>> >
> [mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org<gmod-gbrowse-request <at> lists.sourceforge.net
> <mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>>
>> ]
>> > Sent: Friday, February 26, 2010 10:13 AM
>> > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > Subject: Gmod-gbrowse Digest, Vol 45, Issue 93
>> >
>> > Send Gmod-gbrowse mailing list submissions to
>> >        gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> >        https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > or, via email, send a message with subject or body 'help' to
>> >        gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> >
>> > You can reach the person managing the list at
>> >        gmod-gbrowse-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of Gmod-gbrowse digest..."
>> >
>> >
>> > Today's Topics:
>> >
>> >    1. Re: [Gmod-help] gbrowse_syn (Peter)
>> >   2. Re: gbrowse_img+remote feature (Prem Anand)
>> >   3. Re: gbrowse_img+remote feature (Lincoln Stein)
>> >   4. Re: Slave rendering error (Lincoln Stein)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Fri, 26 Feb 2010 15:47:59 +0000
>> > From: Peter <biopython-amNUQouXnSY2epGFuHBODCp2UmYkHbXO <at> public.gmane.org
> <mailto:biopython-amNUQouXnSY2epGFuHBODCp2UmYkHbXO <at> public.gmane.org>>
>> > Subject: Re: [Gmod-gbrowse] [Gmod-help] gbrowse_syn
>> > To: Michael Paulini <mh6-5fLPn3lgkryFxr2TtlUqVg <at> public.gmane.org <mailto:mh6-5fLPn3lgkryFxr2TtlUqVg <at> public.gmane.org>>
>> > Cc: Chris Fields <cjfields-nzINlOoChub2fBVCVOL8/A <at> public.gmane.org
> <mailto:cjfields-nzINlOoChub2fBVCVOL8/A <at> public.gmane.org>>, mckays-FePsPjn27tw <at> public.gmane.org <mailto:mckays-FePsPjn27tw <at> public.gmane.org>,
>> >         gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > Message-ID:
>> >         <320fb6e01002260747o61f2f667taa57d10917eda9a8-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org
> <mailto:320fb6e01002260747o61f2f667taa57d10917eda9a8-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org>>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > On Fri, Feb 26, 2010 at 3:31 PM, Michael Paulini <mh6-5fLPn3lgkryFxr2TtlUqVg <at> public.gmane.org
> <mailto:mh6-5fLPn3lgkryFxr2TtlUqVg <at> public.gmane.org>>
>> > wrote:
>> > >
>> > > Yup, I do:
>> >
>> > Thanks - it turns out I had seen it before after all, my mistake:
>> > http://lists.open-bio.org/pipermail/open-bio-l/2010-February/000615.html
>> >
>> > Peter
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Fri, 26 Feb 2010 16:05:11 +0000
>> > From: Prem Anand <prem.apa-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org <mailto:prem.apa-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > Subject: Re: [Gmod-gbrowse] gbrowse_img+remote feature
>> > To: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > Message-ID:
>> >         <a38704bf1002260805g6ba6606cvd27036107156631a-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org
> <mailto:a38704bf1002260805g6ba6606cvd27036107156631a-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org>>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Hi Lincoln
>> >
>> > We use 1.70.  Yes when GBrowse is generating the image link, it do
>> > append a
>> > session id, and could see the remote das tracks when the image link is
>> > pasted directly.
>> >
>> > But I am trying to generate the gbrowse_img url through my cgi code and
>> > trying to embed it on the page, not going through gbrowse, as I need to
>> > display a static image, along with some other results.  In this case,
>> > the
>> > remote das track is not getting displayed.  Infact both(local and
>> > remote)
>> > databases are in the same server, but we wanted to split the databases
>> > for
>> > easy maintenance.
>> >
>> > This show the remote das track:
>> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
>> > TRACK;width=800;id=836eafe0a66378536ffb40786a1b561f;keystyle=between;gri
>> > d=on;embed=1
>> >
>> >
>> > Doesn't show:
>> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
>> > TRACK;width=800;keystyle=between;grid=on;embed=1
>> >
>> >
>> > And if both the tracks are local(in the same conf file/single database),
>> > then there is no problem. Both tracks are visible with gbrowse_img call
>> > even
>> > without session id.
>> >
>> > I tried gbgff approach as well, but have other issues with that like
>> > feature->display_name not getting displayed for remote track, so
>> > sticking to
>> > das approach for now.
>> >
>> > Many Thanks for your time,
>> > Prem
>> >
>> >
>> >
>> > On Fri, Feb 26, 2010 at 3:23 PM, Lincoln Stein
>> > <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>wrote:
>> >
>> > > Hi Prem,
>> > >
>> > > Which version of GBrowse are you seeing this behavior in? You do
>> > indeed
>> > > need to append a session ID to the gbrowse_img URL, but gbrowse is
>> > supposed
>> > > to do this for you when it generates the "image" link.
>> > >
>> > > Lincoln
>> > >
>> > >
>> > > On Thu, Feb 25, 2010 at 1:21 PM, Premanand Achuthan <
>> > > Premanand.Achuthan-piTOwl1TIVXQzY9nttDBhA <at> public.gmane.org
> <mailto:Premanand.Achuthan-piTOwl1TIVXQzY9nttDBhA <at> public.gmane.org>> wrote:
>> > >
>> > >> Hi All
>> > >>
>> > >> I have a track that calls a remote feature through das.  The remote
>> > >> track along with other tracks is displayed properly when the call is
>> > >> made through /cgi-bin/gbrowse/.
>> > >> But the remote track alone is not shown (other tracks are shown) if I
>> > >> wanted to generate the gbrowse image via /cgi-bin/gbrowse_img call.
>> > >>
>> > >> Upon examing the gbrowse sessions file, the page_settings is empty
>> > >> $D = {'.source' => '01_Hs_NCBI36','01_Hs_NCBI36' => {'page_settings'
>> > =>
>> > >> {},'plugins'=>........;$D
>> > >> compared to the previous call (cgi-bin/gbrowse)
>> > >>
>> > >> I am able to see the track, if the session id(generated by the first
>> > >> call) is appended to the url, like
>> > >>
>> > >>
>> > /cgi-bin/gbrowse_img/dsn/?name=chr11:2110344..2139147;type=bla+bla+bla;i
>> > d=0fd35a9527c74e5da0d96d4d8aa0651e;other_img_params
>> > >>
>> > >> How to get the proper page_settings in the gbrowse session file for
>> > >> remote tracks?
>> > >>
>> > >> Am I missing something? or doing something wrong?
>> > >>
>> > >> Thanks to Everyone,
>> > >> Prem
>> > >>
>> > >>
>> > >>
>> > ------------------------------------------------------------------------
>> > ------
>> > >> Download Intel® Parallel Studio Eval
>>
>> > >> Try the new software tools for yourself. Speed compiling, find bugs
>> > >> proactively, and fine-tune applications for parallel performance.
>> > >> See why Intel Parallel Studio got high marks during beta.
>> > >> http://p.sf.net/sfu/intel-sw-dev
>> > >> _______________________________________________
>> > >> Gmod-gbrowse mailing list
>> > >> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >>
>> > >
>> > >
>> > >
>> > > --
>> > > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>> > >
>> > >
>> > >
>> > ------------------------------------------------------------------------
>> > ------
>> > > Download Intel® Parallel Studio Eval
>>
>> > > Try the new software tools for yourself. Speed compiling, find bugs
>> > > proactively, and fine-tune applications for parallel performance.
>> > > See why Intel Parallel Studio got high marks during beta.
>> > > http://p.sf.net/sfu/intel-sw-dev
>> > > _______________________________________________
>> > > Gmod-gbrowse mailing list
>> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >
>> > >
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> >
>> > ------------------------------
>> >
>> > Message: 3
>> > Date: Fri, 26 Feb 2010 11:11:02 -0500
>> > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > Subject: Re: [Gmod-gbrowse] gbrowse_img+remote feature
>> > To: Prem Anand <prem.apa-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org <mailto:prem.apa-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > Message-ID:
>> >         <6dce9a0b1002260811h1135ab99ga82c812a7bfb06e-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org
> <mailto:6dce9a0b1002260811h1135ab99ga82c812a7bfb06e-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org>>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > How is the remote track added? Is it added by uploading the URL, or
>> > using
>> > the "remote feature" option in the config file. In the latter case, it
>> > should not be necessary to include the session ID.
>> >
>> > Lincoln
>> >
>> > On Fri, Feb 26, 2010 at 11:05 AM, Prem Anand <prem.apa-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:prem.apa-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>> wrote:
>> >
>> > > Hi Lincoln
>> > >
>> > > We use 1.70.  Yes when GBrowse is generating the image link, it do
>> > append a
>> > > session id, and could see the remote das tracks when the image link is
>> > > pasted directly.
>> > >
>> > > But I am trying to generate the gbrowse_img url through my cgi code
>> > and
>> > > trying to embed it on the page, not going through gbrowse, as I need
>> > to
>> > > display a static image, along with some other results.  In this case,
>> > the
>> > > remote das track is not getting displayed.  Infact both(local and
>> > remote)
>> > > databases are in the same server, but we wanted to split the databases
>> > for
>> > > easy maintenance.
>> > >
>> > > This show the remote das track:
>> > >
>> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
>> > TRACK;width=800;id=836eafe0a66378536ffb40786a1b561f;keystyle=between;gri
>> > d=on;embed=1
>> > >
>> > >
>> > > Doesn't show:
>> > >
>> > /cgi-bin/gbrowse_img/01_Hs_NCBI36/?name=XXX;type=LOCAL_TRACK+REMOTE_DAS_
>> > TRACK;width=800;keystyle=between;grid=on;embed=1
>> > >
>> > >
>> > > And if both the tracks are local(in the same conf file/single
>> > database),
>> > > then there is no problem. Both tracks are visible with gbrowse_img
>> > call even
>> > > without session id.
>> > >
>> > > I tried gbgff approach as well, but have other issues with that like
>> > > feature->display_name not getting displayed for remote track, so
>> > sticking to
>> > > das approach for now.
>> > >
>> > > Many Thanks for your time,
>> > > Prem
>> > >
>> > >
>> > >
>> > > On Fri, Feb 26, 2010 at 3:23 PM, Lincoln Stein
>> > <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>wrote:
>> > >
>> > >> Hi Prem,
>> > >>
>> > >> Which version of GBrowse are you seeing this behavior in? You do
>> > indeed
>> > >> need to append a session ID to the gbrowse_img URL, but gbrowse is
>> > supposed
>> > >> to do this for you when it generates the "image" link.
>> > >>
>> > >> Lincoln
>> > >>
>> > >>
>> > >> On Thu, Feb 25, 2010 at 1:21 PM, Premanand Achuthan <
>> > >> Premanand.Achuthan-piTOwl1TIVXQzY9nttDBhA <at> public.gmane.org
> <mailto:Premanand.Achuthan-piTOwl1TIVXQzY9nttDBhA <at> public.gmane.org>> wrote:
>> > >>
>> > >>> Hi All
>> > >>>
>> > >>> I have a track that calls a remote feature through das.  The remote
>> > >>> track along with other tracks is displayed properly when the call is
>> > >>> made through /cgi-bin/gbrowse/.
>> > >>> But the remote track alone is not shown (other tracks are shown) if
>> > I
>> > >>> wanted to generate the gbrowse image via /cgi-bin/gbrowse_img call.
>> > >>>
>> > >>> Upon examing the gbrowse sessions file, the page_settings is empty
>> > >>> $D = {'.source' => '01_Hs_NCBI36','01_Hs_NCBI36' => {'page_settings'
>> > =>
>> > >>> {},'plugins'=>........;$D
>> > >>> compared to the previous call (cgi-bin/gbrowse)
>> > >>>
>> > >>> I am able to see the track, if the session id(generated by the first
>> > >>> call) is appended to the url, like
>> > >>>
>> > >>>
>> > /cgi-bin/gbrowse_img/dsn/?name=chr11:2110344..2139147;type=bla+bla+bla;i
>> > d=0fd35a9527c74e5da0d96d4d8aa0651e;other_img_params
>> > >>>
>> > >>> How to get the proper page_settings in the gbrowse session file for
>> > >>> remote tracks?
>> > >>>
>> > >>> Am I missing something? or doing something wrong?
>> > >>>
>> > >>> Thanks to Everyone,
>> > >>> Prem
>> > >>>
>> > >>>
>> > >>>
>> > ------------------------------------------------------------------------
>> > ------
>> > >>> Download Intel® Parallel Studio Eval
>>
>> > >>> Try the new software tools for yourself. Speed compiling, find bugs
>> > >>> proactively, and fine-tune applications for parallel performance.
>> > >>> See why Intel Parallel Studio got high marks during beta.
>> > >>> http://p.sf.net/sfu/intel-sw-dev
>> > >>> _______________________________________________
>> > >>> Gmod-gbrowse mailing list
>> > >>> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >>>
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>> > >>
>> > >>
>> > >>
>> > ------------------------------------------------------------------------
>> > ------
>> > >> Download Intel® Parallel Studio Eval
>>
>> > >> Try the new software tools for yourself. Speed compiling, find bugs
>> > >> proactively, and fine-tune applications for parallel performance.
>> > >> See why Intel Parallel Studio got high marks during beta.
>> > >> http://p.sf.net/sfu/intel-sw-dev
>> > >> _______________________________________________
>> > >> Gmod-gbrowse mailing list
>> > >> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >>
>> > >>
>> > >
>> >
>> >
>> > --
>> > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Fri, 26 Feb 2010 11:12:36 -0500
>> > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > Subject: Re: [Gmod-gbrowse] Slave rendering error
>> > To: "Jayararaman, Pushkala" <pjayaraman-gYfhEnJJ71g <at> public.gmane.org
> <mailto:pjayaraman-gYfhEnJJ71g <at> public.gmane.org>>
>> > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > Message-ID:
>> >         <6dce9a0b1002260812te864bf0i647e08360181b422-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org
> <mailto:6dce9a0b1002260812te864bf0i647e08360181b422-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org>>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Hi,
>> >
>> > I am interested in the contents of the gbrowse_slave error log, which is
>> > a
>> > separate error log usually written to /var/log/gbrowse/gbrowse_slave.
>> > The
>> > apache error log is only showing that the slave cannot be reached.
>> >
>> > Lincoln
>> >
>> > On Thu, Feb 25, 2010 at 4:20 PM, Jayararaman, Pushkala
>> > <pjayaraman-gYfhEnJJ71g <at> public.gmane.org <mailto:pjayaraman-gYfhEnJJ71g <at> public.gmane.org>>wrote:
>> >
>> > >  here is the error logs from apache:
>> > >
>> > >
>> > > [Thu Feb 25 15:13:02 2010] [error] [client 127.0.0.1] GBROWSE NOTICE:
>> > To
>> > > enable PDF generation, please enter the directory "/var/www" and run
>> > the
>> > > commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache
>> > .inkscape
>> > > .gnome2".  To turn off this message add "generate pdf = 0" to the
>> > [GENERAL]
>> > > section of your GBrowse.conf configuration file., referer:
>> > > http://localhost/gb2/gbrowse/volvox/?source=volvox
>> > >
>> > r/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphics/
>> > Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > Transp TranslationF with http://127.0.0.1:8103 at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > TranslationR Genes Translation LTRs tRNAs with http://127.0.0.1:8101
>> > at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > TranslationR Genes Translation LTRs tRNAs with http://127.0.0.1:8103
>> > at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > DNA/GC Content ncRNA CDS with http://127.0.0.1:8101 at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:05 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > DNA/GC Content ncRNA CDS with http://127.0.0.1:8102 at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:07 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > GC:region with http://127.0.0.1:8102 at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:07 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > GC:region with http://127.0.0.1:8103 at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > > [Thu Feb 25 15:13:07 2010] [error] [client 127.0.0.1] retrying fetch
>> > of
>> > > Centro:overview with http://127.0.0.1:8102 at
>> > >
>> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux-thread-multi/Bio/Graphi
>> > cs/Browser2/RenderPanels.pm
>> > > line 690., referer:
>> > > http://localhost/gb2/gbrowse/renderfarm/?source=renderfarm
>> > >
>> > >
>> > > There seems to be a problem in the RenderPanels.pm
>> > > The error logs have been consistently pointing to that. How do I work
>> > > around this?
>> > >
>> > >
>> > > Pushkala
>> > >
>> > >
>> > >
>> > > -----Original Message-----
>> > > From: gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org> [
>> > >
> 
>> >
> mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org<gmod-gbrowse-request <at> lists.sourceforge.net
> <mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>>
>> <gmod-gbrowse-request <at> l
>> > ists.sourceforge.net <http://ists.sourceforge.net>>
>> > > ]
>> > > Sent: Thu 2/25/2010 3:14 PM
>> > > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > Subject: Gmod-gbrowse Digest, Vol 45, Issue 86
>> > >
>> > > Send Gmod-gbrowse mailing list submissions to
>> > >         gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > >
>> > > To subscribe or unsubscribe via the World Wide Web, visit
>> > >         https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > > or, via email, send a message with subject or body 'help' to
>> > >         gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > >
>> > > You can reach the person managing the list at
>> > >         gmod-gbrowse-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > >
>> > > When replying, please edit your Subject line so it is more specific
>> > > than "Re: Contents of Gmod-gbrowse digest..."
>> > >
>> > >
>> > > Today's Topics:
>> > >
>> > >    1. gbrowse2 search bug? (Christopher Porter)
>> > >    2. Re: gbrowse2 search bug? (Lincoln Stein)
>> > >    3. (no subject) (Syed Mustafa Hussain)
>> > >    4. loader for GFF3 (Syed Mustafa Hussain)
>> > >    5. Re: gbrowse2 search bug? (Lincoln Stein)
>> > >
>> > >
>> > > ----------------------------------------------------------------------
>> > >
>> > > Message: 1
>> > > Date: Thu, 25 Feb 2010 15:20:33 -0500
>> > > From: Christopher Porter <cporter-V3tf7a8Vaus <at> public.gmane.org <mailto:cporter-V3tf7a8Vaus <at> public.gmane.org>>
>> > > Subject: [Gmod-gbrowse] gbrowse2 search bug?
>> > > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > Message-ID: <7B1B25A5-A956-4355-A455-B283154462DF-V3tf7a8Vaus <at> public.gmane.org
> <mailto:7B1B25A5-A956-4355-A455-B283154462DF-V3tf7a8Vaus <at> public.gmane.org>>
>> > > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>> > >
>> > >
>> > > Gbrowse 2.0 is returning an error when I search for a chromosomal
>> > > region under a specific set of circumstances - is this a known
>> > > problem, or is there a configuration option I can change to make this
>> > > go away?
>> > >
>> > > To reproduce the error:
>> > >
>> > > 1) Search for a gene using a partial gene symbol (e.g. Pou) which will
>> > > return a list of genes matching the name (autocomplete on).
>> > > 2) Select one of the returned genes by clicking on the gene symbol.
>> > >
>> > > After doing this, any subsequent search by location will return the
>> > > error "The landmark named chr1:167805616..167865031 is not recognized.
>> > > See the help pages for suggestions". This happens both for searches
>> > > using the 'landmark or region' search field, or using a ?
>> > > name=<location> URL. As far as I can tell, this can only be resolved
>> > > by hitting the 'Reset' link, after which location searches work again.
>> > >
>> > > Selecting the location link at step (2) doesn't result in the error-
>> > > prone state being set.
>> > >
>> > > Running gbrowse2 (2.0) with mysql backend plus BAM flatfiles; scaffold
>> > > is mouse genomic sequence.
>> > >
>> > > Any suggestions?
>> > >
>> > > Thanks,
>> > >
>> > > Chris
>> > >
>> > >
>> > > --------------------
>> > > Confidentiality Statement - The contents of this e-mail, including its
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>> > > contain confidential or privileged information.  If you are not the
>> > intended
>> > > recipient, you are strictly prohibited from reading, using,
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>> > > immediately or the Privacy Office (privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK <at> public.gmane.org
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>> > > permanently delete this e-mail and its attachments, along with any
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>> > > thereof.  Thank you.
>> > >
>> > > Avis de confidentialit? - Ce courriel, y compris ses pi?ces jointes,
>> > > s'adresse au destinataire uniquement et pourrait contenir des
>> > renseignements
>> > > confidentiels. Si vous n'?tes pas le bon destinataire, il est
>> > strictement
>> > > interdit de lire, d'utiliser, de divulguer, de copier ou de diffuser
>> > ce
>> > > courriel ou son contenu, en partie ou en entier. Si vous avez re?u ce
>> > > courriel par erreur, veuillez en informer imm?diatement l'exp?diteur
>> > ou le
>> > > bureau de la Protection des renseignements personnels (
>> > > info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys <at> public.gmane.org
> <mailto:info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys <at> public.gmane.org>), puis effacez le courriel
> ainsi que
>> > les
>> > > pi?ces jointes et toute autre copie. Merci.
>> > > --------------------
>> > >
>> > >
>> > >
>> > > ------------------------------
>> > >
>> > > Message: 2
>> > > Date: Thu, 25 Feb 2010 16:04:27 -0500
>> > > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > > Subject: Re: [Gmod-gbrowse] gbrowse2 search bug?
>> > > To: Christopher Porter <cporter-V3tf7a8Vaus <at> public.gmane.org <mailto:cporter-V3tf7a8Vaus <at> public.gmane.org>>
>> > > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > Message-ID:
>> > >        
> <6dce9a0b1002251304g11805485g5d604012a6cddac1-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org
> <mailto:6dce9a0b1002251304g11805485g5d604012a6cddac1-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org>>
>> > > Content-Type: text/plain; charset="windows-1252"
>> > >
>> > > This is a known problem and I am working on it.
>> > >
>> > > Lincoln
>> > >
>> > > On Thu, Feb 25, 2010 at 3:20 PM, Christopher Porter
> <cporter-V3tf7a8Vaus <at> public.gmane.org <mailto:cporter-V3tf7a8Vaus <at> public.gmane.org>>
>> > > wrote:
>> > >
>> > > >
>> > > > Gbrowse 2.0 is returning an error when I search for a chromosomal
>> > region
>> > > > under a specific set of circumstances - is this a known problem, or
>> > is
>> > > there
>> > > > a configuration option I can change to make this go away?
>> > > >
>> > > > To reproduce the error:
>> > > >
>> > > > 1) Search for a gene using a partial gene symbol (e.g. Pou) which
>> > will
>> > > > return a list of genes matching the name (autocomplete on).
>> > > > 2) Select one of the returned genes by clicking on the gene symbol.
>> > > >
>> > > > After doing this, any subsequent search by location will return the
>> > error
>> > > > "The landmark named chr1:167805616..167865031 is not recognized. See
>> > the
>> > > > help pages for suggestions". This happens both for searches using
>> > the
>> > > > 'landmark or region' search field, or using a ?name=<location> URL.
>> > As
>> > > far
>> > > > as I can tell, this can only be resolved by hitting the 'Reset'
>> > link,
>> > > after
>> > > > which location searches work again.
>> > > >
>> > > > Selecting the location link at step (2) doesn't result in the
>> > error-prone
>> > > > state being set.
>> > > >
>> > > > Running gbrowse2 (2.0) with mysql backend plus BAM flatfiles;
>> > scaffold is
>> > > > mouse genomic sequence.
>> > > >
>> > > > Any suggestions?
>> > > >
>> > > > Thanks,
>> > > >
>> > > > Chris
>> > > >
>> > > >
>> > > > --------------------
>> > > > Confidentiality Statement - The contents of this e-mail, including
>> > its
>> > > > attachment, are intended for the exclusive use of the recipient and
>> > may
>> > > > contain confidential or privileged information.  If you are not the
>> > > intended
>> > > > recipient, you are strictly prohibited from reading, using,
>> > disclosing,
>> > > > copying, or distributing this e-mail or any of its contents.  If you
>> > > > received this e-mail in error, please notify the sender by reply
>> > e-mail
>> > > > immediately or the Privacy Office (privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK <at> public.gmane.org
> <mailto:privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK <at> public.gmane.org> )
>> > and
>> > > > permanently delete this e-mail and its attachments, along with any
>> > copies
>> > > > thereof.  Thank you.
>> > > >
>> > > > Avis de confidentialit? ? Ce courriel, y compris ses pi?ces jointes,
>> > > > s?adresse au destinataire uniquement et pourrait contenir des
>> > > renseignements
>> > > > confidentiels. Si vous n??tes pas le bon destinataire, il est
>> > strictement
>> > > > interdit de lire, d?utiliser, de divulguer, de copier ou de diffuser
>> > ce
>> > > > courriel ou son contenu, en partie ou en entier. Si vous avez re?u
>> > ce
>> > > > courriel par erreur, veuillez en informer imm?diatement l?exp?diteur
>> > ou
>> > > le
>> > > > bureau de la Protection des renseignements personnels (
>> > > > info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys <at> public.gmane.org
> <mailto:info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys <at> public.gmane.org>), puis effacez le courriel
> ainsi que
>> > les
>> > > > pi?ces jointes et toute autre copie. Merci.
>> > > > --------------------
>> > > >
>> > > >
>> > > >
>> > > >
>> > >
>> > ------------------------------------------------------------------------
>> > ------
>> > > > Download Intel? Parallel Studio Eval
>> > > > Try the new software tools for yourself. Speed compiling, find bugs
>> > > > proactively, and fine-tune applications for parallel performance.
>> > > > See why Intel Parallel Studio got high marks during beta.
>> > > > http://p.sf.net/sfu/intel-sw-dev
>> > > > _______________________________________________
>> > > > Gmod-gbrowse mailing list
>> > > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > > >
>> > > >
>> > >
>> > >
>> > > --
>> > > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>> > > -------------- next part --------------
>> > > An HTML attachment was scrubbed...
>> > >
>> > > ------------------------------
>> > >
>> > > Message: 3
>> > > Date: Thu, 25 Feb 2010 13:07:13 -0800 (PST)
>> > > From: Syed Mustafa Hussain <comp_sea-/E1597aS9LQAvxtiuMwx3w <at> public.gmane.org
> <mailto:comp_sea-/E1597aS9LQAvxtiuMwx3w <at> public.gmane.org>>
>> > > Subject: [Gmod-gbrowse] (no subject)
>> > > To: Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > Message-ID: <141654.38826.qm-XCd8ux6whGmvuULXzWHTWIglqE1Y4D90QQ4Iyu8u01E <at> public.gmane.org
> <mailto:141654.38826.qm-XCd8ux6whGmvuULXzWHTWIglqE1Y4D90QQ4Iyu8u01E <at> public.gmane.org>>
>> > > Content-Type: text/plain; charset=us-ascii
>> > >
>> > > Hi,
>> > >
>> > > Does someone knows a loader which is faster than
>> > bp_seqfeature_load.PLS and
>> > > create database for Bio::DB::SeqFeature::Store adaptor. I have nearly
>> > 100GB
>> > > SNP data to load and currently I am using bp_seqfeature_load.PLS which
>> > is
>> > > kind of slow. I cannot use bulk_load_gff.PLS/fast_load_gff.PLS because
>> > it
>> > > create database for Bio::DB::GFF adaptor, for which using aggregators
>> > are
>> > > not convenient.
>> > >
>> > > Or, is there a way to tweak bulk_load_gff.PLS/fast_load_gff.PLS to
>> > create
>> > > database for Bio::DB::SeqFeature::Store adaptor.
>> > >
>> > > Thanks,
>> > > Mustafa.
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > ------------------------------
>> > >
>> > > Message: 4
>> > > Date: Thu, 25 Feb 2010 12:42:25 -0800 (PST)
>> > > From: Syed Mustafa Hussain <comp_sea-/E1597aS9LQAvxtiuMwx3w <at> public.gmane.org
> <mailto:comp_sea-/E1597aS9LQAvxtiuMwx3w <at> public.gmane.org>>
>> > > Subject: [Gmod-gbrowse] loader for GFF3
>> > > To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > Message-ID: <728670.61633.qm-FlipYfUoLlOvuULXzWHTWIglqE1Y4D90QQ4Iyu8u01E <at> public.gmane.org
> <mailto:728670.61633.qm-FlipYfUoLlOvuULXzWHTWIglqE1Y4D90QQ4Iyu8u01E <at> public.gmane.org>>
>> > > Content-Type: text/plain; charset="us-ascii"
>> > >
>> > > Hi,
>> > >
>> > > Does someone knows a loader which is faster than
>> > bp_seqfeature_load.PLS and
>> > > create database for Bio::DB::SeqFeature::Store adaptor. I have nearly
>> > 100GB
>> > > SNP data to load and currently I am using bp_seqfeature_load.PLS which
>> > is
>> > > kind of slow. I cannot use bulk_load_gff.PLS/fast_load_gff.PLS because
>> > it
>> > > create database for Bio::DB::GFF adaptor, for which using aggregators
>> > are
>> > > not convenient.
>> > >
>> > > Or, is there a way to tweak bulk_load_gff.PLS/fast_load_gff.PLS to
>> > create
>> > > database for Bio::DB::SeqFeature::Store adaptor.
>> > >
>> > > Thanks,
>> > > Mustafa.
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > -------------- next part --------------
>> > > An HTML attachment was scrubbed...
>> > >
>> > > ------------------------------
>> > >
>> > > Message: 5
>> > > Date: Thu, 25 Feb 2010 16:14:43 -0500
>> > > From: Lincoln Stein <lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org
> <mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w <at> public.gmane.org>>
>> > > Subject: Re: [Gmod-gbrowse] gbrowse2 search bug?
>> > > To: Christopher Porter <cporter-V3tf7a8Vaus <at> public.gmane.org <mailto:cporter-V3tf7a8Vaus <at> public.gmane.org>>
>> > > Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > Message-ID:
>> > >        
> <6dce9a0b1002251314h72810ae6ua93a50719de2b7dd-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org
> <mailto:6dce9a0b1002251314h72810ae6ua93a50719de2b7dd-JsoAwUIsXosN+BqQ9rBEUg <at> public.gmane.org>>
>> > > Content-Type: text/plain; charset="windows-1252"
>> > >
>> > > Hi Chris,
>> > >
>> > > Could you see what happens when you set the BAM databases search
>> > options to
>> > > "none"?
>> > >
>> > > Lincoln
>> > >
>> > > On Thu, Feb 25, 2010 at 3:20 PM, Christopher Porter
> <cporter-V3tf7a8Vaus <at> public.gmane.org <mailto:cporter-V3tf7a8Vaus <at> public.gmane.org>>
>> > > wrote:
>> > >
>> > > >
>> > > > Gbrowse 2.0 is returning an error when I search for a chromosomal
>> > region
>> > > > under a specific set of circumstances - is this a known problem, or
>> > is
>> > > there
>> > > > a configuration option I can change to make this go away?
>> > > >
>> > > > To reproduce the error:
>> > > >
>> > > > 1) Search for a gene using a partial gene symbol (e.g. Pou) which
>> > will
>> > > > return a list of genes matching the name (autocomplete on).
>> > > > 2) Select one of the returned genes by clicking on the gene symbol.
>> > > >
>> > > > After doing this, any subsequent search by location will return the
>> > error
>> > > > "The landmark named chr1:167805616..167865031 is not recognized. See
>> > the
>> > > > help pages for suggestions". This happens both for searches using
>> > the
>> > > > 'landmark or region' search field, or using a ?name=<location> URL.
>> > As
>> > > far
>> > > > as I can tell, this can only be resolved by hitting the 'Reset'
>> > link,
>> > > after
>> > > > which location searches work again.
>> > > >
>> > > > Selecting the location link at step (2) doesn't result in the
>> > error-prone
>> > > > state being set.
>> > > >
>> > > > Running gbrowse2 (2.0) with mysql backend plus BAM flatfiles;
>> > scaffold is
>> > > > mouse genomic sequence.
>> > > >
>> > > > Any suggestions?
>> > > >
>> > > > Thanks,
>> > > >
>> > > > Chris
>> > > >
>> > > >
>> > > > --------------------
>> > > > Confidentiality Statement - The contents of this e-mail, including
>> > its
>> > > > attachment, are intended for the exclusive use of the recipient and
>> > may
>> > > > contain confidential or privileged information.  If you are not the
>> > > intended
>> > > > recipient, you are strictly prohibited from reading, using,
>> > disclosing,
>> > > > copying, or distributing this e-mail or any of its contents.  If you
>> > > > received this e-mail in error, please notify the sender by reply
>> > e-mail
>> > > > immediately or the Privacy Office (privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK <at> public.gmane.org
> <mailto:privacy-YIe52a3VE2wN1z1Zqg7UwhX4PxoxT+RK <at> public.gmane.org> )
>> > and
>> > > > permanently delete this e-mail and its attachments, along with any
>> > copies
>> > > > thereof.  Thank you.
>> > > >
>> > > > Avis de confidentialit? ? Ce courriel, y compris ses pi?ces jointes,
>> > > > s?adresse au destinataire uniquement et pourrait contenir des
>> > > renseignements
>> > > > confidentiels. Si vous n??tes pas le bon destinataire, il est
>> > strictement
>> > > > interdit de lire, d?utiliser, de divulguer, de copier ou de diffuser
>> > ce
>> > > > courriel ou son contenu, en partie ou en entier. Si vous avez re?u
>> > ce
>> > > > courriel par erreur, veuillez en informer imm?diatement l?exp?diteur
>> > ou
>> > > le
>> > > > bureau de la Protection des renseignements personnels (
>> > > > info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys <at> public.gmane.org
> <mailto:info.privee-XAT+ERpYCxIrWLYXXyNtbywD8/FfD2ys <at> public.gmane.org>), puis effacez le courriel
> ainsi que
>> > les
>> > > > pi?ces jointes et toute autre copie. Merci.
>> > > > --------------------
>> > > >
>> > > >
>> > > >
>> > > >
>> > >
>> > ------------------------------------------------------------------------
>> > ------
>> > > > Download Intel? Parallel Studio Eval
>> > > > Try the new software tools for yourself. Speed compiling, find bugs
>> > > > proactively, and fine-tune applications for parallel performance.
>> > > > See why Intel Parallel Studio got high marks during beta.
>> > > > http://p.sf.net/sfu/intel-sw-dev
>> > > > _______________________________________________
>> > > > Gmod-gbrowse mailing list
>> > > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > > >
>> > > >
>> > >
>> > >
>> > > --
>> > > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>> > > -------------- next part --------------
>> > > An HTML attachment was scrubbed...
>> > >
>> > > ------------------------------
>> > >
>> > >
>> > >
>> > ------------------------------------------------------------------------
>> > ------
>> > > Download Intel? Parallel Studio Eval
>> > > Try the new software tools for yourself. Speed compiling, find bugs
>> > > proactively, and fine-tune applications for parallel performance.
>> > > See why Intel Parallel Studio got high marks during beta.
>> > > http://p.sf.net/sfu/intel-sw-dev
>> > >
>> > > ------------------------------
>> > >
>> > > _______________________________________________
>> > > Gmod-gbrowse mailing list
>> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >
>> > >
>> > > End of Gmod-gbrowse Digest, Vol 45, Issue 86
>> > > ********************************************
>> > >
>> > >
>> > >
>> > >
>> > ------------------------------------------------------------------------
>> > ------
>> > > Download Intel® Parallel Studio Eval
>>
>> > > Try the new software tools for yourself. Speed compiling, find bugs
>> > > proactively, and fine-tune applications for parallel performance.
>> > > See why Intel Parallel Studio got high marks during beta.
>> > > http://p.sf.net/sfu/intel-sw-dev
>> > > _______________________________________________
>> > > Gmod-gbrowse mailing list
>> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >
>> > >
>> >
>> >
>> > --
>> > 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> >
>> > ------------------------------
>> >
>> > ------------------------------------------------------------------------
>> > ------
>> > Download Intel® Parallel Studio Eval
>> > Try the new software tools for yourself. Speed compiling, find bugs
>> > proactively, and fine-tune applications for parallel performance.
>> > See why Intel Parallel Studio got high marks during beta.
>> > http://p.sf.net/sfu/intel-sw-dev
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>> > End of Gmod-gbrowse Digest, Vol 45, Issue 93
>> > ********************************************
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>>
>> > Download Intel® Parallel Studio Eval
>> > Try the new software tools for yourself. Speed compiling, find bugs
>> > proactively, and fine-tune applications for parallel performance.
>> > See why Intel Parallel Studio got high marks during beta.
>> > http://p.sf.net/sfu/intel-sw-dev
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> <mailto:Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org>
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>>
>>
>>
>> --
>> 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
>>
>>
> 
> 
> --
> 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
> 
> 
> 
> 
> -- 
> 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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org
> <mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q <at> public.gmane.org>>
> 
> 
> 
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> 
> 
> 
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f <at> public.gmane.org
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev

Gmane