Nabble - gmod-gbrowse

Re: GBrowse2 - intermittently truncated read track for NGS data

2009-11-12T07:58:05Z

Hi Lincoln,

I am just running GBrowse as a CGI script at the moment. I gave up on
mod_perl when I noticed the problem with the truncated tracks.

Relevant software versions:

Gbrowse - svn trunk rev. 22245
Samtools - svn trunk rev. 510
Bio::SamTools - svn trunk rev. 22246

I also tried rebuilding Bio::SamTools with Samtools v 0.1.6, but the
problem persists.

The system is a quad-core Xeon w/ Ubuntu 9.04.

-Scott

On Thu, Nov 12, 2009 at 11:41 AM, Lincoln Stein <lincoln.stein@...> wrote:

> Hi Scott,
>
> Are you running GBrowse as a CGI script or under fastCGI or mod_perl? My
> guess is that there is some sort of issue with buffering in the samtools
> library, because gbrowse tries to reuse filehandles whenever possible, but
> this should only show up when GBrowse is running as a single-threaded
> process under fastCGI.
>
> I haven't seen this problem myself, so unless I can reproduce it locally, I
> may have to send you proposed patches and debugging statements to help track
> down the problem. Can you tell me exactly what version of GBrowse, samtools
> and Bio::SamTools you are seeing this phenomenon with?
>
> Lincoln
>
> On Thu, Nov 12, 2009 at 10:07 AM, Scott Perry <scperry@...> wrote:
>>
>> Hi Scott,
>>
>> The problem appears to be related to having multiple tracks based on
>> the same BAM file.
>>
>> If I just use a single track, there are never any display problems. If
>> I add a second track and use the same db_adaptor, one of the tracks is
>> intermittently truncated. It is quite repeatable.
>>
>> I am able to work around the problem by creating a copy of my
>> BAM/reference/index files, and then using a second db_adaptor based on
>> the duplicate copies. As long as I limit each db_adaptor to a single
>> track, everything seems fine.
>>
>> Any ideas?
>>
>> -Scott
>>
>>
>>
>> On Thu, Nov 12, 2009 at 10:35 AM, Scott Cain <scott@...> wrote:
>> > Hi Scott,
>> >
>> > I wonder if you a running out of memory or temp space?
>> >
>> > Scott
>> >
>> > On Thu, Nov 12, 2009 at 1:32 AM, Scott Perry <scperry@...> wrote:
>> >> Hello,
>> >>
>> >> I recently installed GBrowse2, Bio::DB:Sam, and Samtools from svn, and
>> >> I
>> >> have noticed an intermittent issue with the read-related tracks.
>> >>
>> >> When I try to view a BWA-generated alignment in GBrowse, the read track
>> >> and
>> >> read coverage tracks are occasionally truncated (see attachment). No
>> >> errors
>> >> show up in the Apache error log, although I have noticed a few
>> >> gbrowse-related segfaults in /var/log/messages. GBrowse does not appear
>> >> to
>> >> segfault every time the tracks appear truncated, though.
>> >>
>> >> I added an additional read track to my config to illustrate the
>> >> problem.
>> >> Sometimes the tracks appear in their entirety, while subsequent clicks
>> >> on
>> >> the 'search' button will eventually lead to the appearance of partial
>> >> tracks..
>> >>
>> >> The problem occurs more often when viewing a region of about 20,000bp
>> >> or
>> >> greater, although I have seen it occur in smaller regions as well.
>> >>
>> >> Is there any sort of debugging mode that I can enable in order to
>> >> isolate
>> >> the problem?
>> >>
>> >> Thanks,
>> >>
>> >> -Scott
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> >> 30-Day
>> >> trial. Simplify your report design, integration and deployment - and
>> >> focus
>> >> on
>> >> what you do best, core application coding. Discover what's new with
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>> >> _______________________________________________
>> >> 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
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
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>
>
>
> --
> 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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Re: ggb 1.71b using DAS server for the fasta sequences

2009-11-12T07:56:42Z

Hi Marc,

Each server will need a database that provides the names of the chromosomes and their lengths. This can be a flat GFF file, or any of the adapters that GBrowse supports. You do not need to provide the full FASTA file with the sequence unless the browser needs to display the sequence for GC content, stop sites, etc.

Lincoln

On Thu, Nov 5, 2009 at 11:57 AM, Marc Wessner <mwessner@...> wrote:

Hi,

I have to install many private genome browsers that display specific
annotations on the human genome.

I intend to configure a DAS server that could provide all the human
common tracks for all my genome browsers, so I don't have to copy the
whole genome fasta files and mRNA tracks data etc... several times.
First of all, am I right or the fasta files have to be present in each
browser database ?

In a browser that shall use the DAS server (but doesn't yet), I have
only loaded a few gff files : chromosome.gff, cytobands.gff and the
annotations.
Without the fasta files, when I try this genome browser alone, I get an
error message that says:"chr?start:end reference is unknown!" (what ever
the figures may be)

Am I missing something ?
I am using this documentation:
http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#DAS
Shall I look anywhere else ?

Where could I find an explanation of how the region is defined:
- Is chromosome.gff not enough to display the annotations for a given
region (I am not talking about bases or GC%) ?
- Are fasta file madatory for such a purpose ?
- Can the fasta sequences be part of what is gotten from the DAS in
order (I hope so)?

Thanks for your hints,

Best regards

Marc

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--
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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Re: GBrowse2 - intermittently truncated read track for NGS data

2009-11-12T07:41:02Z

Hi Scott,

Are you running GBrowse as a CGI script or under fastCGI or mod_perl? My guess is that there is some sort of issue with buffering in the samtools library, because gbrowse tries to reuse filehandles whenever possible, but this should only show up when GBrowse is running as a single-threaded process under fastCGI.

I haven't seen this problem myself, so unless I can reproduce it locally, I may have to send you proposed patches and debugging statements to help track down the problem. Can you tell me exactly what version of GBrowse, samtools and Bio::SamTools you are seeing this phenomenon with?

Lincoln

On Thu, Nov 12, 2009 at 10:07 AM, Scott Perry <scperry@...> wrote:

Hi Scott,

The problem appears to be related to having multiple tracks based on
the same BAM file.

If I just use a single track, there are never any display problems. If
I add a second track and use the same db_adaptor, one of the tracks is
intermittently truncated. It is quite repeatable.

I am able to work around the problem by creating a copy of my
BAM/reference/index files, and then using a second db_adaptor based on
the duplicate copies. As long as I limit each db_adaptor to a single
track, everything seems fine.

Any ideas?

-Scott

On Thu, Nov 12, 2009 at 10:35 AM, Scott Cain <scott@...> wrote:
> Hi Scott,
>
> I wonder if you a running out of memory or temp space?
>
> Scott
>
> On Thu, Nov 12, 2009 at 1:32 AM, Scott Perry <scperry@...> wrote:
>> Hello,
>>
>> I recently installed GBrowse2, Bio::DB:Sam, and Samtools from svn, and I
>> have noticed an intermittent issue with the read-related tracks.
>>
>> When I try to view a BWA-generated alignment in GBrowse, the read track and
>> read coverage tracks are occasionally truncated (see attachment). No errors
>> show up in the Apache error log, although I have noticed a few
>> gbrowse-related segfaults in /var/log/messages. GBrowse does not appear to
>> segfault every time the tracks appear truncated, though.
>>
>> I added an additional read track to my config to illustrate the problem.
>> Sometimes the tracks appear in their entirety, while subsequent clicks on
>> the 'search' button will eventually lead to the appearance of partial
>> tracks..
>>
>> The problem occurs more often when viewing a region of about 20,000bp or
>> greater, although I have seen it occur in smaller regions as well.
>>
>> Is there any sort of debugging mode that I can enable in order to isolate
>> the problem?
>>
>> Thanks,
>>
>> -Scott
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> 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
>

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Re: GBrowse2 - intermittently truncated read track for NGS data

2009-11-12T07:07:24Z

Hi Scott,

The problem appears to be related to having multiple tracks based on
the same BAM file.

If I just use a single track, there are never any display problems. If
I add a second track and use the same db_adaptor, one of the tracks is
intermittently truncated. It is quite repeatable.

I am able to work around the problem by creating a copy of my
BAM/reference/index files, and then using a second db_adaptor based on
the duplicate copies. As long as I limit each db_adaptor to a single
track, everything seems fine.

Any ideas?

-Scott

On Thu, Nov 12, 2009 at 10:35 AM, Scott Cain <scott@...> wrote:

> Hi Scott,
>
> I wonder if you a running out of memory or temp space?
>
> Scott
>
> On Thu, Nov 12, 2009 at 1:32 AM, Scott Perry <scperry@...> wrote:
>> Hello,
>>
>> I recently installed GBrowse2, Bio::DB:Sam, and Samtools from svn, and I
>> have noticed an intermittent issue with the read-related tracks.
>>
>> When I try to view a BWA-generated alignment in GBrowse, the read track and
>> read coverage tracks are occasionally truncated (see attachment). No errors
>> show up in the Apache error log, although I have noticed a few
>> gbrowse-related segfaults in /var/log/messages. GBrowse does not appear to
>> segfault every time the tracks appear truncated, though.
>>
>> I added an additional read track to my config to illustrate the problem.
>> Sometimes the tracks appear in their entirety, while subsequent clicks on
>> the 'search' button will eventually lead to the appearance of partial
>> tracks..
>>
>> The problem occurs more often when viewing a region of about 20,000bp or
>> greater, although I have seen it occur in smaller regions as well.
>>
>> Is there any sort of debugging mode that I can enable in order to isolate
>> the problem?
>>
>> Thanks,
>>
>> -Scott
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> 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
>

Re: GBrowse2 - how to remove outline around features

2009-11-12T06:47:47Z

Hi Scott,
I am using the heatmap glyph. Some of my features withing the track are only 1-2 bps. So when they are outlined (i did set bgcolor and fgcolor to be the same), and I am viewing more than 200bp at a time, all I end up seeing is the bg/fgcolour for these features. This is not the case in version 1.69, only in version 2.

Thanks for your help,
Liisa

Scott Cain <scott@...>

2009-11-11 22:23

To	Liisa Koski <liisa.koski@...>
cc	gmod-gbrowse@...
Subject	Re: [Gmod-gbrowse] GBrowse2 - how to remove outline around features

Hi Lisa, I think setting fgcolor equal to the same thing as your bgcolor will do what you want, assuming I understand you correctly. Scott On Wed, Nov 11, 2009 at 8:22 AM, Liisa Koski <liisa.koski@...> wrote: > > Hello, > I'm using GBrowse2 and would like to remove the line around my features in a > track. I tried setting linewidth=0 but this did not have any effect. In > Gbrowse1.69 I do not have a line around my features and I think I am using a > similar configuration. > > Thanks for your help, > Liisa > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > 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

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Re: GBrowse2 - intermittently truncated read track for NGS data

2009-11-12T06:35:21Z

Hi Scott,

I wonder if you a running out of memory or temp space?

Scott

On Thu, Nov 12, 2009 at 1:32 AM, Scott Perry <scperry@...> wrote:

> Hello,
>
> I recently installed GBrowse2, Bio::DB:Sam, and Samtools from svn, and I
> have noticed an intermittent issue with the read-related tracks.
>
> When I try to view a BWA-generated alignment in GBrowse, the read track and
> read coverage tracks are occasionally truncated (see attachment). No errors
> show up in the Apache error log, although I have noticed a few
> gbrowse-related segfaults in /var/log/messages. GBrowse does not appear to
> segfault every time the tracks appear truncated, though.
>
> I added an additional read track to my config to illustrate the problem.
> Sometimes the tracks appear in their entirety, while subsequent clicks on
> the 'search' button will eventually lead to the appearance of partial
> tracks..
>
> The problem occurs more often when viewing a region of about 20,000bp or
> greater, although I have seen it occur in smaller regions as well.
>
> Is there any sort of debugging mode that I can enable in order to isolate
> the problem?
>
> Thanks,
>
> -Scott
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> 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

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Re: DNA sequence callback

2009-11-12T06:33:27Z

Hi Miquel,

IIRC, the trick is that the dna method returns a Bio::Seq object, not
a dna string. To get the dna string, you have to call the seq method
on it, so like this:

my $refseq = $self->dna->seq;

Scott

2009/11/10 Miquel Ràmia <miquel.ramia@...>:

> Hi,
>
> I'm trying to show the reference nucleotide sequence for some features
> in a balloon popup. I've tryed with a callback using:
>
> $self = shift;
> $refseq = $self->dna;
>
> but it's not working, how can I do it ?
>
> thank you very much
>
> Miquel Ramia
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
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>

Re: ask for a help

2009-11-12T06:29:26Z

Please keep replies on the list.

OK, but you still don't have a read track, only remark. Have you added tracks to your configuration file that match up with your data?

On Thu, Nov 12, 2009 at 12:05 AM, liyan0316 <liyan0316@...> wrote:

This is my gff3 files, one is TAIR's gff3 file, the other is write by myself totally. They both didn't work.

The gff3 file writed by myself is

##gff-version 3

##Index-subfeatures 1

Chr1 bowtie chromosome 1 28914870 . . . Name=Chr1;

Chr1 bowtie reads 25007555 25007597 . + . Name=2

Chr1 bowtie reads 9753677 9753719 . - . Name=3

Chr1 bowtie reads 9092439 9092481 . + . Name=11

Chr1 bowtie reads 9048629 9048671 . + . Name=17

Chr1 bowtie reads 7911737 7911779 . + . Name=25

Chr1 bowtie reads 28914828 28914870 . + . Name=26

Chr1 bowtie reads 20192981 20193023 . + . Name=30

Chr1 bowtie reads 28782558 28782600 . + . Name=31

Chr1 bowtie reads 19716743 19716785 . - . Name=32

Chr1 bowtie reads 26819643 26819685 . - . Name=33

Chr1 bowtie reads 21773727 21773769 . - . Name=37

Chr2 bowtie chromosome 1 28914870 . . . ID=Chr2;Name=Chr2

Chr2 bowtie reads 11763945 11763987 . - . Name=5

Chr2 bowtie reads 12006936 12006978 . + . Name=8

Chr2 bowtie reads 14224401 14224443 . + . Name=12

Chr2 bowtie reads 16296349 16296391 . - . Name=27

Chr2 bowtie reads 3248783 3248825 . - . Name=28

Chr2 bowtie reads 4188371 4188413 . + . Name=34

Chr3 bowtie chromosome 1 28914870 . . . ID=Chr3;Name=Chr3

Chr3 bowtie reads 19102078 19102120 . - . Name=4

Chr3 bowtie reads 13594789 13594831 . + . Name=7

Chr3 bowtie reads 22066138 22066180 . + . Name=9

Chr3 bowtie reads 3657949 3657991 . + . Name=13

Chr3 bowtie reads 19138413 19138455 . - . Name=14

Chr3 bowtie reads 19298969 19299011 . - . Name=16

Chr3 bowtie reads 20994600 20994642 . + . Name=36

2009-11-12

liyan0316

发件人： Scott Cain

发送时间： 2009-11-12 12:50:27

收件人： liyan0316

抄送： gmod-gbrowse

主题： Re: [Gmod-gbrowse] ask for a help

Hi Liyan,

Do you have any 'remark' features in your arabidopsis gff3 file? Have you added a track stanza for the genes in the file?

Scott

On Fri, Nov 6, 2009 at 2:42 AM, liyan0316 <liyan0316@...> wrote:

I want to look arabidopsis genome, so I write arabidopsis.conf and gff3 file, but it can't display genes in any region.

yeast and volvox display nomally. It should have problems in arabidopsis.conf or gff3.

but I don't know how to fix them.

thank you

here is my conf file...

[GENERAL]

description   = arabidopsis TAIR8

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor memory

-dir 'C:/Program Files/Apache Software Foundation/Apache2.2/htdocs/gbrowse/databases/arabidopsis'

plugins       =

drag and drop       = 1

balloon tips        = 0

titles are balloons = 0

# list of tracks to turn on by default

default features = ExampleFeatures

# examples to show in the introduction

examples = Chr1

# what image widths to offer

image widths  = 450 640 800 1024

# default width of detailed view (pixels)

default width = 800

# Web site configuration info

stylesheet  = /gbrowse/gbrowse.css

buttons     = /gbrowse/images/buttons

tmpimages   = /gbrowse/tmp

# feature to show on startup

initial landmark = chr1:1..10000

# max and default segment sizes for detailed view

max segment     = 50000

default segment = 5000

# zoom levels

zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 50000

# colors of the overview, detailed map and key

overview bgcolor = lightgrey

detailed bgcolor = lightgoldenrodyellow

key bgcolor      = beige

label density = 25

bump density  = 100

# "automatic" classes to try when an unqualified identifier is given

automatic classes =

# other customization options...

# HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS

# inside the <head></head> section

head =

# at the top...

header =

# a footer

footer = <hr /><pre>$Id: arabidopsis.conf,v 1.8.8.1.2.4 2008/08/07 16:00:08 scottcain Exp $</pre>

# Various places where you can insert your own HTML -- see configuration docs

html1 =

html2 =

html3 =

html4 =

html5 =

html6 =

category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic'

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100

# where to link to when user clicks in detailed view

link          = AUTO

################## TRACK CONFIGURATION ####################

# the remainder of the sections configure individual tracks

###########################################################

[ExampleFeatures]

feature      = remark

glyph        = generic

stranded     = 1

bgcolor      = blue

height       = 10

key          = Example Features

#[Chromosome:overview]

#feature = chromosome

#bgcolor        = lightslategray

#glyph          = generic

#fgcolor        = black

#height         = 8

#point          = 1

#citation       = This track shows the entire chromosome.  A vertical red line shows the position of the detail view below.

#key            = Chromosome

2009-11-06

liyan0316

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

Re: Upgrading Gbrowse2

2009-11-12T05:01:25Z

Hi Miquel,

If you modified files that GBrowse installed, then yes, you would lose
the changes. You would be better off making copies of those files and
modifying the copies, then having the configuration files point at the
copies (for css files) or using the modified glyphs for your track
config.

Scott

2009/11/10 Miquel Ràmia <miquel.ramia@...>:

> Hello,
>
> I want to upgrade my Gbrowse 1.996 to 1.997 , but I've some files with
> modifications like gliphs and style sheets.. will they be lost if I
> upgrade? Which is the best option to upgrade it ?
>
> Kind reggards
>
> Miquel Ràmia
>
>
> ------------------------------------------------------------------------------
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Re: DNA sequence callback

2009-11-11T22:52:41Z

Hi Miquel,

If my Perl were better I might be able to tell you. I'm attaching two
routines from the dna glyph that I'm hoping will make it easy for you
(or people with better Perl than mine) to figure out how to display
the sequence. The dna glyph shows bases at high magnifications, and
%gc at lower magnifications.

Dave C

sub draw_component {
my $self = shift;
my $gd = shift;
my ($x1,$y1,$x2,$y2) = $self->bounds(@_);

my $dna = eval { $self->feature->seq };
$dna = $dna->seq if ref($dna) and $dna->can('seq'); # to
catch Bio::PrimarySeqI objects
$dna or return;

# workaround for my misreading of interface -- LS
$dna = $dna->seq if ref($dna) && $dna->can('seq');

if ($self->dna_fits) {
$self->draw_dna($gd,$dna,$x1,$y1,$x2,$y2);
} elsif ($self->do_gc) {
$self->draw_gc_content($gd,$dna,$x1,$y1,$x2,$y2);
}
}

sub draw_dna {
my $self = shift;

my ($gd,$dna,$x1,$y1,$x2,$y2) = @_;
my $pixels_per_base = $self->scale;
my $feature = $self->feature;

my $strand = $feature->strand || 1;
$strand *= -1 if $self->{flip};

my @bases = split '',$strand >= 0 ? $dna : $self->reversec($dna);

my $color = $self->fgcolor;
my $font = $self->font;
my $lineheight = $font->height;
$y1 -= $lineheight/2 - 3;
my $strands = $self->option('strand') || 'auto';

my ($forward,$reverse);
if ($strands eq 'auto') {
$forward = $feature->strand >= 0;
$reverse = $feature->strand <= 0;
} elsif ($strands eq 'both') {
$forward = $reverse = 1;
} elsif ($strands eq 'reverse') {
$reverse = 1;
} else {
$forward = 1;
}
# minus strand features align right, not left
$x1 += $pixels_per_base - $font->width - 1 if $strand < 0;
for (my $i=0;$i<@bases;$i++) {
my $x = $x1 + $i * $pixels_per_base;
$gd->char($font,$x+2,$y1,$bases[$i],$color)
if $forward;
$gd->char($font,$x+2,$y1+($forward ? $lineheight:0),
$complement{$bases[$i]}||$bases[$i],$color)
if $reverse;
}

}

2009/11/10 Miquel Ràmia <miquel.ramia@...>:

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GBrowse2 - intermittently truncated read track for NGS data

2009-11-11T22:32:39Z

Hello,

I recently installed GBrowse2, Bio::DB:Sam, and Samtools from svn, and I
have noticed an intermittent issue with the read-related tracks.

When I try to view a BWA-generated alignment in GBrowse, the read track
and read coverage tracks are occasionally truncated (see attachment). No
errors show up in the Apache error log, although I have noticed a few
gbrowse-related segfaults in /var/log/messages. GBrowse does not appear
to segfault every time the tracks appear truncated, though.

I added an additional read track to my config to illustrate the problem.
Sometimes the tracks appear in their entirety, while subsequent clicks
on the 'search' button will eventually lead to the appearance of partial
tracks..

The problem occurs more often when viewing a region of about 20,000bp or
greater, although I have seen it occur in smaller regions as well.

Is there any sort of debugging mode that I can enable in order to
isolate the problem?

Thanks,

-Scott

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gbrowse_ngs_read_display_issues.png (57K) Download Attachment

Re: ggb 1.71b using DAS server for the fasta sequences

2009-11-11T20:09:50Z

To add to this, and answer one of your other questions: you do not
absolutely need to have the dna sequences themselves to make gbrowse
work: all you really need is a gff file that describes the features.
You only need the dna sequence if you want to use the dna/gc content
glyph or provide translations either for the translation glyph or in
the cds glyph.

Scott

On Mon, Nov 9, 2009 at 5:54 PM, Dave Clements, GMOD Help Desk
<help@...> wrote:

> Hi Marc,
>
> I'm not an experienced DAS person, but I might be able to shed some
> light on the error message. I believe the "chr?start:end reference is
> unknown!" error message is the result of not defining the whole
> chromosome somewhere. From the tutorial
> (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#data_file):
>
> ---
> It is very important to have a full-length entry (such as the one for
> ctgA) for each reference sequence mentioned in the first column of the
> GFF3 file. However, the reference sequence can have any source and
> type you choose. Commonly used types are "clone", "chromosome" and
> "contig."
> ---
>
> I *think* you need to define the overall chromosome in a local database.
>
> Does anyone else have suggestions?
>
> Thanks,
>
> Dave C.
>
>
> On Thu, Nov 5, 2009 at 8:57 AM, Marc Wessner <mwessner@...> wrote:
>> Hi,
>>
>> I have to install many private genome browsers that display specific
>> annotations on the human genome.
>>
>> I intend to configure a DAS server that could provide all the human
>> common tracks for all my genome browsers, so I don't have to copy the
>> whole genome fasta files and mRNA tracks data etc... several times.
>> First of all, am I right or the fasta files have to be present in each
>> browser database ?
>>
>> In a browser that shall use the DAS server (but doesn't yet), I have
>> only loaded a few gff files : chromosome.gff, cytobands.gff and the
>> annotations.
>> Without the fasta files, when I try this genome browser alone, I get an
>> error message that says:"chr?start:end reference is unknown!" (what ever
>> the figures may be)
>>
>> Am I missing something ?
>> I am using this documentation:
>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#DAS
>> Shall I look anywhere else ?
>>
>> Where could I find an explanation of how the region is defined:
>> - Is chromosome.gff not enough to display the annotations for a given
>> region (I am not talking about bases or GC%) ?
>> - Are fasta file madatory for such a purpose ?
>> - Can the fasta sequences be part of what is gotten from the DAS in
>> order (I hope so)?
>>
>> Thanks for your hints,
>>
>> Best regards
>>
>> Marc
>>
>>
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>>
>
>
>
> --
> Please keep responses on the list!
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> http://gmod.org/wiki/GMOD_News
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Re: ask for a help

2009-11-11T20:03:08Z

Hi Liyan,

Do you have any 'remark' features in your arabidopsis gff3 file? Have you added a track stanza for the genes in the file?

Scott

On Fri, Nov 6, 2009 at 2:42 AM, liyan0316 <liyan0316@...> wrote:

I want to look arabidopsis genome, so I write arabidopsis.conf and gff3 file, but it can't display genes in any region.

yeast and volvox display nomally. It should have problems in arabidopsis.conf or gff3.

but I don't know how to fix them.

thank you

here is my conf file...

[GENERAL]

description   = arabidopsis TAIR8

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor memory

-dir 'C:/Program Files/Apache Software Foundation/Apache2.2/htdocs/gbrowse/databases/arabidopsis'

plugins       =

drag and drop       = 1

balloon tips        = 0

titles are balloons = 0

# list of tracks to turn on by default

default features = ExampleFeatures

# examples to show in the introduction

examples = Chr1

# what image widths to offer

image widths  = 450 640 800 1024

# default width of detailed view (pixels)

default width = 800

# Web site configuration info

stylesheet  = /gbrowse/gbrowse.css

buttons     = /gbrowse/images/buttons

tmpimages   = /gbrowse/tmp

# feature to show on startup

initial landmark = chr1:1..10000

# max and default segment sizes for detailed view

max segment     = 50000

default segment = 5000

# zoom levels

zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 50000

# colors of the overview, detailed map and key

overview bgcolor = lightgrey

detailed bgcolor = lightgoldenrodyellow

key bgcolor      = beige

label density = 25

bump density  = 100

# "automatic" classes to try when an unqualified identifier is given

automatic classes =

# other customization options...

# HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS

# inside the <head></head> section

head =

# at the top...

header =

# a footer

footer = <hr /><pre>$Id: arabidopsis.conf,v 1.8.8.1.2.4 2008/08/07 16:00:08 scottcain Exp $</pre>

# Various places where you can insert your own HTML -- see configuration docs

html1 =

html2 =

html3 =

html4 =

html5 =

html6 =

category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic'

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100

# where to link to when user clicks in detailed view

link          = AUTO

################## TRACK CONFIGURATION ####################

# the remainder of the sections configure individual tracks

###########################################################

[ExampleFeatures]

feature      = remark

glyph        = generic

stranded     = 1

bgcolor      = blue

height       = 10

key          = Example Features

#[Chromosome:overview]

#feature = chromosome

#bgcolor        = lightslategray

#glyph          = generic

#fgcolor        = black

#height         = 8

#point          = 1

#citation       = This track shows the entire chromosome.  A vertical red line shows the position of the detail view below.

#key            = Chromosome

2009-11-06

liyan0316

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Re: GBrowse2 - how to remove outline around features

2009-11-11T19:23:48Z

>
> Hello,
> I'm using GBrowse2 and would like to remove the line around my features in a
> track. I tried setting linewidth=0 but this did not have any effect. In
> Gbrowse1.69 I do not have a line around my features and I think I am using a
> similar configuration.
>
> Thanks for your help,
> Liisa
>
>
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>

Re: Build test on gbrowse2 fails

2009-11-11T18:54:37Z

Dave Clements, GMOD Help Desk wrote:
> Hi Wes,
>
> I'm guessing from subsequent emails that you got past this problem?

I updated all of the ExtUtils perl modules. I then did a new SVN
checkout of gbrowse2 and got this revision:

# Checked out revision 22245.

The ./Build test step hangs here:

Copying sample_data/yeast_scaffolds/chromosomes.gff3 -> blib/database/yeast_scaffolds/chromosomes.gff3
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... 1/90 Can't locate object method "parse_fh" via package "Bio::Graphics::Browser2::DataSource" at
/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 981.
t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 4/90 subtests
t/03.render.t ............. 45/148 invalid track Motif at /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/Render.pm line 1828.
*** glibc detected *** double free or corruption (!prev): 0x0b5d62d8 ***

I had received this same error/hang a few weeks and and posted a question
but did not receive any responses.

Does this error mean anything to anyone?

> Thanks,
>
> Dave C
>
> On Mon, Nov 9, 2009 at 3:59 PM, Wes Barris <wes.barris@...> wrote:
>> Hi,
>>
>> I am getting this error when running Build test on a freshly downloaded
>> copy of gbrowse2:
>>
>> wes@bioweb> sudo ./Build test
>> NOTE: Run ./Build reconfig to change existing configuration.
>> .
>> .
>> .
>> gcc -I/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/libalign -I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE -DXS_VERSION="1.9971" -DVERSION="1.9971" -fPIC -c -D_REENTRANT
>> -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -o
>> lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
>> lib/Bio/Graphics/Browser2/CAlign.c: In function `boot_Bio__Graphics__Browser2__CAlign':
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: `PL_unitcheckav' undeclared (first use in this function)
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: (Each undeclared identifier is reported only once
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: for each function it appears in.)
>> error building lib/Bio/Graphics/Browser2/CAlign.o from 'lib/Bio/Graphics/Browser2/CAlign.c' at /usr/lib/perl5/site_perl/5.8.5/ExtUtils/CBuilder/Base.pm line 110.
>>
>> Is gbrowse2 in a buildable state right now?
>> --
>> Wes Barris <wes.barris@...>
>>
>> ------------------------------------------------------------------------------
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>
>
>

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Re: Build test on gbrowse2 fails

2009-11-11T17:02:43Z

Dave Clements, GMOD Help Desk wrote:
> Hi Wes,
>
> I'm guessing from subsequent emails that you got past this problem?

Hi Dave,

No, I have not got past this. I am unable to build gbrowse2.

Re: Build test on gbrowse2 fails

2009-11-11T16:24:52Z

Hi Wes,

I'm guessing from subsequent emails that you got past this problem?

Thanks,

Dave C

On Mon, Nov 9, 2009 at 3:59 PM, Wes Barris <wes.barris@...> wrote:

> Hi,
>
> I am getting this error when running Build test on a freshly downloaded
> copy of gbrowse2:
>
> wes@bioweb> sudo ./Build test
> NOTE: Run ./Build reconfig to change existing configuration.
> .
> .
> .
> gcc -I/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/libalign -I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE -DXS_VERSION="1.9971" -DVERSION="1.9971" -fPIC -c -D_REENTRANT
> -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -o
> lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
> lib/Bio/Graphics/Browser2/CAlign.c: In function `boot_Bio__Graphics__Browser2__CAlign':
> lib/Bio/Graphics/Browser2/CAlign.c:295: error: `PL_unitcheckav' undeclared (first use in this function)
> lib/Bio/Graphics/Browser2/CAlign.c:295: error: (Each undeclared identifier is reported only once
> lib/Bio/Graphics/Browser2/CAlign.c:295: error: for each function it appears in.)
> error building lib/Bio/Graphics/Browser2/CAlign.o from 'lib/Bio/Graphics/Browser2/CAlign.c' at /usr/lib/perl5/site_perl/5.8.5/ExtUtils/CBuilder/Base.pm line 110.
>
> Is gbrowse2 in a buildable state right now?
> --
> Wes Barris <wes.barris@...>
>
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Re: [Gmod-help] general questions about data querying

2009-11-11T14:24:44Z

Dear Ryan, Dave etc.,

This is the sort if thing I do lots of, but using GFF files and perl code.
Often the perl code is a simple one-liner. If your GFF file is sorted
by location, finding overlapped genes with opposite strand is easy:

cat genes.gff | grep mRNA | perl -ne\
'($c,$t,$s,$b,$e,$p,$o)=split; if($c eq $lc and $b<$le and $o ne $lo){print "<$lgene>$_";}\
($lc,$lb,$le,$lo,$lgene)=($c,$b,$e,$o,$_);' | more

.. or maybe you want to grep exon types, or UTRs here
.. if your .gff isn't location sorted,
cat genes.gff | sort -k1,1 -k4,4n -k5,5nr | ..

You can do this in a mysql database, with sql code, but there are so many
useful sorts of pattern matching and greping with perl and unix that I find
that much easier for genome processing and analyses.

- Don

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Re: [Gmod-help] general questions about data querying

2009-11-11T14:20:25Z

Hi Dave and Ryan,

Right--both Bio::DB::GFF and Bio::DB::SeqFeature::Store support
querying via the perl API. You can look at the perldoc for simple
examples of what can be done, and you can look at this WormBase page:

http://www.wormbase.org/wiki/index.php/Mining_WormBase_with_Bio::DB::GFF

for more complex examples. While those examples are using
Bio::DB::GFF, SeqFeature::Store supports most of the same method calls.

Scott

On Nov 11, 2009, at 5:08 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Ryan,
>
> GFF3 is stored in the Sequence module in Chado, which is fairly well
> documented. See http://gmod.org/wiki/Chado_Sequence_Module for a
> start.
>
> You *can* query the Bio::DB::SeqFeature::Store directly, but I don't
> think that format is as well documented. You'll also (I think) have
> to use Perl since features are stored in a binary Perl format.
>
> Dave C.
>
> On Wed, Nov 11, 2009 at 1:51 PM, Ryan Golhar <golharam@...>
> wrote:
>> Hi Dave. Thanks for the response.
>>
>> I guess my problem comes down to "I know what I'm looking for", now
>> I need
>> to scan through the coordinates of the genes to find the ones that
>> overlap.
>> I figured I could readily query the database the same way Gbrowse
>> does to
>> get at the data, is that a correct approach? I suppose querying the
>> database is a better solution than querying GBrowse as Gbrowse is
>> just
>> displaying the data from the database, correct?
>>
>> If I load the data into Chado (I currently have it in GFF in
>> mySQL), then
>> how to I query the database?
>>
>> Once I have all the data processed, I will end up creating a gff
>> file and
>> displaying it in GBrowse, but I need to get the data first...
>>
>> Ryan
>>
>>
>> Dave Clements, GMOD Help Desk wrote:
>>>
>>> The next best thing is for sites to define their own set of
>>> interesting questions and run some preprocessing on the data to find
>>> regions that are "interesting". There are several ways to display
>>> and/or link to interesting regions. There could be a separate page
>>> that lists them; on any feature that is interesting the popup/hover
>>> could have a link to "show other +/- strand overlapping genes". If
>>> there aren't too many of them you could have a track in the overview
>>> or region areas that shows the interesting areas and then users
>>> could
>>> zoom in on them.
>>>
>>>
>>> Hmm. I just reread your email, and you *might* be asking a
>>> different
>>> question. Do you want to ask this question in the database itself,
>>> rather than in GBrowse? To do this, I would load the data into
>>> Chado
>>> and ask it there. The databases that usually back GBrowse are built
>>> for speed, rather than for clarity and ad hoc questions.
>>>
>>>
>>> Hopefully, I answered your question, and your next question
>>> too. ;-)
>>>
>>> I also encourage anyone else on the list to respond.
>>>
>>> Dave C.
>>>
>>>
>>> On Wed, Nov 11, 2009 at 12:42 PM, Ryan Golhar <golharam@...>
>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I recently installed Gbrowse to view some data I have, but now I'm
>>>> interested in performing a more thorough analysis of the data. I
>>>> want to
>>>> identify certain regions of the genome that contain overlapping
>>>> genes on
>>>> the plus/minus strand ie one gene on the plus strand and a 2nd
>>>> gene on
>>>> the
>>>> minus strand overlapping the 1st gene.
>>>>
>>>> I can see one or two of these occurrences in GBrowse, but I don't
>>>> want to
>>>> do
>>>> this manually. Is there a way to query the database to find all
>>>> occurrences
>>>> of these?
>>>>
>>>> Ryan
>>>>
>>>
>>>
>>>
>>
>
>
>
> --
> Please keep responses on the list!
> http://gmod.org/wiki/January_2010_GMOD_Meeting
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-help] general questions about data querying

2009-11-11T14:08:13Z

Hi Ryan,

GFF3 is stored in the Sequence module in Chado, which is fairly well
documented. See http://gmod.org/wiki/Chado_Sequence_Module for a
start.

You *can* query the Bio::DB::SeqFeature::Store directly, but I don't
think that format is as well documented. You'll also (I think) have
to use Perl since features are stored in a binary Perl format.

Dave C.

On Wed, Nov 11, 2009 at 1:51 PM, Ryan Golhar <golharam@...> wrote:

> Hi Dave. Thanks for the response.
>
> I guess my problem comes down to "I know what I'm looking for", now I need
> to scan through the coordinates of the genes to find the ones that overlap.
> I figured I could readily query the database the same way Gbrowse does to
> get at the data, is that a correct approach? I suppose querying the
> database is a better solution than querying GBrowse as Gbrowse is just
> displaying the data from the database, correct?
>
> If I load the data into Chado (I currently have it in GFF in mySQL), then
> how to I query the database?
>
> Once I have all the data processed, I will end up creating a gff file and
> displaying it in GBrowse, but I need to get the data first...
>
> Ryan
>
>
> Dave Clements, GMOD Help Desk wrote:
>>
>> The next best thing is for sites to define their own set of
>> interesting questions and run some preprocessing on the data to find
>> regions that are "interesting". There are several ways to display
>> and/or link to interesting regions. There could be a separate page
>> that lists them; on any feature that is interesting the popup/hover
>> could have a link to "show other +/- strand overlapping genes". If
>> there aren't too many of them you could have a track in the overview
>> or region areas that shows the interesting areas and then users could
>> zoom in on them.
>>
>>
>> Hmm. I just reread your email, and you *might* be asking a different
>> question. Do you want to ask this question in the database itself,
>> rather than in GBrowse? To do this, I would load the data into Chado
>> and ask it there. The databases that usually back GBrowse are built
>> for speed, rather than for clarity and ad hoc questions.
>>
>>
>> Hopefully, I answered your question, and your next question too. ;-)
>>
>> I also encourage anyone else on the list to respond.
>>
>> Dave C.
>>
>>
>> On Wed, Nov 11, 2009 at 12:42 PM, Ryan Golhar <golharam@...> wrote:
>>>
>>> Hi,
>>>
>>> I recently installed Gbrowse to view some data I have, but now I'm
>>> interested in performing a more thorough analysis of the data. I want to
>>> identify certain regions of the genome that contain overlapping genes on
>>> the plus/minus strand ie one gene on the plus strand and a 2nd gene on
>>> the
>>> minus strand overlapping the 1st gene.
>>>
>>> I can see one or two of these occurrences in GBrowse, but I don't want to
>>> do
>>> this manually. Is there a way to query the database to find all
>>> occurrences
>>> of these?
>>>
>>> Ryan
>>>
>>
>>
>>
>

Re: [Gmod-help] general questions about data querying

2009-11-11T13:51:33Z

Hi Dave. Thanks for the response.

I guess my problem comes down to "I know what I'm looking for", now I
need to scan through the coordinates of the genes to find the ones that
overlap. I figured I could readily query the database the same way
Gbrowse does to get at the data, is that a correct approach? I suppose
querying the database is a better solution than querying GBrowse as
Gbrowse is just displaying the data from the database, correct?

If I load the data into Chado (I currently have it in GFF in mySQL),
then how to I query the database?

Once I have all the data processed, I will end up creating a gff file
and displaying it in GBrowse, but I need to get the data first...

Ryan

Dave Clements, GMOD Help Desk wrote:

> The next best thing is for sites to define their own set of
> interesting questions and run some preprocessing on the data to find
> regions that are "interesting". There are several ways to display
> and/or link to interesting regions. There could be a separate page
> that lists them; on any feature that is interesting the popup/hover
> could have a link to "show other +/- strand overlapping genes". If
> there aren't too many of them you could have a track in the overview
> or region areas that shows the interesting areas and then users could
> zoom in on them.
>
>
> Hmm. I just reread your email, and you *might* be asking a different
> question. Do you want to ask this question in the database itself,
> rather than in GBrowse? To do this, I would load the data into Chado
> and ask it there. The databases that usually back GBrowse are built
> for speed, rather than for clarity and ad hoc questions.
>
>
> Hopefully, I answered your question, and your next question too. ;-)
>
> I also encourage anyone else on the list to respond.
>
> Dave C.
>
>
> On Wed, Nov 11, 2009 at 12:42 PM, Ryan Golhar <golharam@...> wrote:
>> Hi,
>>
>> I recently installed Gbrowse to view some data I have, but now I'm
>> interested in performing a more thorough analysis of the data. I want to
>> identify certain regions of the genome that contain overlapping genes on
>> the plus/minus strand ie one gene on the plus strand and a 2nd gene on the
>> minus strand overlapping the 1st gene.
>>
>> I can see one or two of these occurrences in GBrowse, but I don't want to do
>> this manually. Is there a way to query the database to find all occurrences
>> of these?
>>
>> Ryan
>>
>
>
>

Re: [Gmod-help] general questions about data querying

2009-11-11T13:41:23Z

Hi Ryan,

I'm CC'ing the GBrowse list as I often get questions like this at
conferences. I think this is worth a general discussion.

There are a couple of widely used mechanisms for locating information
in GBrowse: coordinates, names, BLAST. GBrowse does not have a
mechanism for asking "Show me other regions that look like this
region", where "look like" is determined at run time based on
displayed features in the selected region. That would be ideal, but
as you can imagine, it would also be a *lot* of work requiring both
research and coding. (Anyone out there need to do a thesis?)

The next best thing is for sites to define their own set of
interesting questions and run some preprocessing on the data to find
regions that are "interesting". There are several ways to display
and/or link to interesting regions. There could be a separate page
that lists them; on any feature that is interesting the popup/hover
could have a link to "show other +/- strand overlapping genes". If
there aren't too many of them you could have a track in the overview
or region areas that shows the interesting areas and then users could
zoom in on them.

Hmm. I just reread your email, and you *might* be asking a different
question. Do you want to ask this question in the database itself,
rather than in GBrowse? To do this, I would load the data into Chado
and ask it there. The databases that usually back GBrowse are built
for speed, rather than for clarity and ad hoc questions.

Hopefully, I answered your question, and your next question too. ;-)

I also encourage anyone else on the list to respond.

Dave C.

On Wed, Nov 11, 2009 at 12:42 PM, Ryan Golhar <golharam@...> wrote:

> Hi,
>
> I recently installed Gbrowse to view some data I have, but now I'm
> interested in performing a more thorough analysis of the data. I want to
> identify certain regions of the genome that contain overlapping genes on
> the plus/minus strand ie one gene on the plus strand and a 2nd gene on the
> minus strand overlapping the 1st gene.
>
> I can see one or two of these occurrences in GBrowse, but I don't want to do
> this manually. Is there a way to query the database to find all occurrences
> of these?
>
> Ryan
>

Re: Links from Glyphs on GBrowse 1.70

2009-11-11T11:19:15Z

Hi Ellen,

That helps a lot. I remember having a conversation with Lincoln and
Sheldon about this "fix", but given your suggestion, I'll talk with
them again about whether this is a better alternative.

Thanks,
Scott

On Wed, Nov 11, 2009 at 2:08 PM, <Ellen.Adlem@...> wrote:

> Hi Scott,
>
> An example of what I am talking about can be seen at this link:-
> http://www.t1dbase.org/cgi-bin/gbrowse/01_Hs_NCBI36/?name=chr2%3A204440754..204446928;label=T1DBASE_Regions%3Aoverview-T1DBASE_regions%3Aregion-KARYOTYPE%3Aoverview-KARYOTYPE%3Aregion-CANDIDATE_GENES%3Aregion-GENE_MODEL_ENSEMBL-ENSEMBL_TRANS-GENE_MODEL_T1DBASE
>
> The EnsEMBL transcripts and the T1DBase gene should link out, but the
> image map is not working properly.
>
> Clicking on the draggable tracks option at the bottom restores the links
> correctly.
>
> BTW - this is still using the 1.70 tagged version of Browser.pm (version
> 1.167.4.34.2.32.2.125) and not the updated one from early september
> (version 1.167.4.34.2.32.2.126) , which does restore the links, but you
> have to loose the rubber banding, which we don't want to do.
>
> Does that help?
>
> Cheers,
> Ellen.
>
>
>
>> Hi Ellen,
>>
>> Your suggested fix seems quite reasonable, but I'm a little unclear on
>> what we're trying to fix. Is the problem that there are no links or
>> the links are broken when draggable tracks are turned off or on via
>> the user interface? I just want to verifiy the continuing existence
>> of the bug before I fix it.
>>
>> Thanks,
>> Scott
>>
>>
>> On Wed, Nov 11, 2009 at 12:01 PM, Ellen Adlem
>> <ellen.adlem@...> wrote:
>>> We have been having issues with the links form the Glyphs in the details
>>> section not working due to draggable tracks not being requested in URLs.
>>> I have found that there was a fix done to Browser.pm that fixes this
>>> but at the expense of the rubber banding, so I guess it's kinda fixed.
>>>
>>> However, in investigating this I noticed something in the gbrowse
>>> cgi-bin script that means it overwrites whatever is set in the conf
>>> file. The line given below (line #688 in my file):-
>>>
>>> drag_n_drop => $page_settings->{drag_and_drop}||0,
>>>
>>> means that gbrowse never checks the status of drag and drop in the conf
>>> file, so if the drag_n_drop=1 attribute is not passed in the URL,
>>> draggable tracks are turned off by default.
>>>
>>> Would it be possible to change the above line to read:-
>>>
>>> drag_n_drop =>
>>> $page_settings->{drag_and_drop}||$CONFIG->drag_and_drop||0,
>>>
>>> so that it checks the default in the conf file, if this has been
>>> provided?
>>>
>>> Hope that makes sense?
>>>
>>> Many thanks,
>>> Ellen.
>>>
>>> --
>>> ellen.adlem@...
>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
>>> Cambridge Institute for Medical Research (CIMR)
>>> Wellcome Trust/MRC Building
>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
>>> focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> 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
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>

Re: Links from Glyphs on GBrowse 1.70

2009-11-11T11:08:57Z

Hi Scott,

An example of what I am talking about can be seen at this link:-
http://www.t1dbase.org/cgi-bin/gbrowse/01_Hs_NCBI36/?name=chr2%3A204440754..204446928;label=T1DBASE_Regions%3Aoverview-T1DBASE_regions%3Aregion-KARYOTYPE%3Aoverview-KARYOTYPE%3Aregion-CANDIDATE_GENES%3Aregion-GENE_MODEL_ENSEMBL-ENSEMBL_TRANS-GENE_MODEL_T1DBASE

The EnsEMBL transcripts and the T1DBase gene should link out, but the
image map is not working properly.

Clicking on the draggable tracks option at the bottom restores the links
correctly.

BTW - this is still using the 1.70 tagged version of Browser.pm (version
1.167.4.34.2.32.2.125) and not the updated one from early september
(version 1.167.4.34.2.32.2.126) , which does restore the links, but you
have to loose the rubber banding, which we don't want to do.

Does that help?

Cheers,
Ellen.

> Hi Ellen,
>
> Your suggested fix seems quite reasonable, but I'm a little unclear on
> what we're trying to fix. Is the problem that there are no links or
> the links are broken when draggable tracks are turned off or on via
> the user interface? I just want to verifiy the continuing existence
> of the bug before I fix it.
>
> Thanks,
> Scott
>
>
> On Wed, Nov 11, 2009 at 12:01 PM, Ellen Adlem
> <ellen.adlem@...> wrote:
>> We have been having issues with the links form the Glyphs in the details
>> section not working due to draggable tracks not being requested in URLs.
>> I have found that there was a fix done to Browser.pm that fixes this
>> but at the expense of the rubber banding, so I guess it's kinda fixed.
>>
>> However, in investigating this I noticed something in the gbrowse
>> cgi-bin script that means it overwrites whatever is set in the conf
>> file. The line given below (line #688 in my file):-
>>
>> drag_n_drop => $page_settings->{drag_and_drop}||0,
>>
>> means that gbrowse never checks the status of drag and drop in the conf
>> file, so if the drag_n_drop=1 attribute is not passed in the URL,
>> draggable tracks are turned off by default.
>>
>> Would it be possible to change the above line to read:-
>>
>> drag_n_drop =>
>> $page_settings->{drag_and_drop}||$CONFIG->drag_and_drop||0,
>>
>> so that it checks the default in the conf file, if this has been
>> provided?
>>
>> Hope that makes sense?
>>
>> Many thanks,
>> Ellen.
>>
>> --
>> ellen.adlem@...
>> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
>> Cambridge Institute for Medical Research (CIMR)
>> Wellcome Trust/MRC Building
>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and
>> focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

Re: Links from Glyphs on GBrowse 1.70

2009-11-11T10:30:26Z

Hi Ellen,

Your suggested fix seems quite reasonable, but I'm a little unclear on
what we're trying to fix. Is the problem that there are no links or
the links are broken when draggable tracks are turned off or on via
the user interface? I just want to verifiy the continuing existence
of the bug before I fix it.

Thanks,
Scott

On Wed, Nov 11, 2009 at 12:01 PM, Ellen Adlem
<ellen.adlem@...> wrote:

> We have been having issues with the links form the Glyphs in the details
> section not working due to draggable tracks not being requested in URLs.
> I have found that there was a fix done to Browser.pm that fixes this
> but at the expense of the rubber banding, so I guess it's kinda fixed.
>
> However, in investigating this I noticed something in the gbrowse
> cgi-bin script that means it overwrites whatever is set in the conf
> file. The line given below (line #688 in my file):-
>
> drag_n_drop => $page_settings->{drag_and_drop}||0,
>
> means that gbrowse never checks the status of drag and drop in the conf
> file, so if the drag_n_drop=1 attribute is not passed in the URL,
> draggable tracks are turned off by default.
>
> Would it be possible to change the above line to read:-
>
> drag_n_drop => $page_settings->{drag_and_drop}||$CONFIG->drag_and_drop||0,
>
> so that it checks the default in the conf file, if this has been provided?
>
> Hope that makes sense?
>
> Many thanks,
> Ellen.
>
> --
> ellen.adlem@...
> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
> Cambridge Institute for Medical Research (CIMR)
> Wellcome Trust/MRC Building
> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

Re: Exonerate and GFF3 for GBrowse??

2009-11-11T09:58:04Z

Thanks, Jason. I didn't want to bug you until I needed it ... getting the Exonerate data in has been on the back burner for some time.

In any case, I'll download this as well.

Congrats, btw, on the faculty job!

Best,
Bob

On Nov 11, 2009, at 2:43 AM, Jason Stajich wrote:

sorry bob - I am guessing don's will work fine. some things are

defunct when my former inst stopped supporting some of my websites.

trying to migrate important things to git when I am reminded they are

misising - this folder has some variants of that script in there

including a + and - bioperl one.

http://github.com/hyphaltip/genome-scripts/tree/master/data_format/

-jason

On Nov 9, 2009, at 3:45 PM, Bob Freeman wrote:

Thanks, Don. You're a life saver. All the links pointing to Jason's

old script are dead. Either that, or I haven't search far enough.

-b

On Nov 9, 2009, at 5:38 PM, Don Gilbert wrote:

Bob,

Jason Stajich wrote a useful process_exonerate_gff3 perl; I've a

variant of that

I use, here:

http://eugenes.org/gmod/genogrid/scripts/process_exonerate_gff3.perl

which avoids use of bioperl and is somewhat faster.

- Don Gilbert

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405

-- gilbertd@...--http://marmot.bio.indiana.edu/

-----------------------------------------------------

Bob Freeman, Ph.D.

Acorn Worm Informatics, Kirschner lab

Dept of Systems Biology, Alpert 524

Harvard Medical School

200 Longwood Avenue

Boston, MA 02115

617/432.2293, vox

The only other person I've apologized to is my mother and that was court ordered.

-- Karen Walker from Will & Grace

Links from Glyphs on GBrowse 1.70

2009-11-11T09:01:23Z

We have been having issues with the links form the Glyphs in the details
section not working due to draggable tracks not being requested in URLs.
I have found that there was a fix done to Browser.pm that fixes this
but at the expense of the rubber banding, so I guess it's kinda fixed.

However, in investigating this I noticed something in the gbrowse
cgi-bin script that means it overwrites whatever is set in the conf
file. The line given below (line #688 in my file):-

drag_n_drop => $page_settings->{drag_and_drop}||0,

means that gbrowse never checks the status of drag and drop in the conf
file, so if the drag_n_drop=1 attribute is not passed in the URL,
draggable tracks are turned off by default.

Would it be possible to change the above line to read:-

drag_n_drop => $page_settings->{drag_and_drop}||$CONFIG->drag_and_drop||0,

so that it checks the default in the conf file, if this has been provided?

Hope that makes sense?

Many thanks,
Ellen.

--
ellen.adlem@...
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
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Gmod-gbrowse@...
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directionality in SAM reads

2009-11-11T08:26:42Z

Hello,

Can the reads in SAM format display strandedness information? I know
in tview the reads will show capital letters for forward strand, and
small letters for reverse. I don't think this happens in gbrowse.
Also, at the view where the reads turn from letters into blocks, can
the reads show directionality arrows? Changing "stranded=1" doesn't
seem to accomplish this.

Nicole

------------------------------------------------------------------------------
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trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
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GBrowse2 - how to remove outline around features

2009-11-11T05:22:06Z

Hello,
I'm using GBrowse2 and would like to remove the line around my features in a track. I tried setting linewidth=0 but this did not have any effect. In Gbrowse1.69 I do not have a line around my features and I think I am using a similar configuration.

Thanks for your help,
Liisa

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
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Re: Exonerate and GFF3 for GBrowse??

2009-11-10T23:43:45Z

sorry bob - I am guessing don's will work fine. some things are
defunct when my former inst stopped supporting some of my websites.

trying to migrate important things to git when I am reminded they are
misising - this folder has some variants of that script in there
including a + and - bioperl one.
http://github.com/hyphaltip/genome-scripts/tree/master/data_format/

-jason
On Nov 9, 2009, at 3:45 PM, Bob Freeman wrote:

> Thanks, Don. You're a life saver. All the links pointing to Jason's
> old script are dead. Either that, or I haven't search far enough.
>
> -b
>
> On Nov 9, 2009, at 5:38 PM, Don Gilbert wrote:
>
>>
>> Bob,
>>
>> Jason Stajich wrote a useful process_exonerate_gff3 perl; I've a
>> variant of that
>> I use, here:
>> http://eugenes.org/gmod/genogrid/scripts/process_exonerate_gff3.perl
>> which avoids use of bioperl and is somewhat faster.
>>
>> - Don Gilbert
>> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
>> -- gilbertd@...--http://marmot.bio.indiana.edu/
>
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> Acorn Worm Informatics, Kirschner lab
> Dept of Systems Biology, Alpert 524
> Harvard Medical School
> 200 Longwood Avenue
> Boston, MA 02115
> 617/432.2293, vox
>
> The only other person I've apologized to is my mother and that was
> court ordered.
> -- Karen Walker from Will & Grace
>
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-Day
> trial. Simplify your report design, integration and deployment - and
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Jason Stajich
jason.stajich@...
jason@...

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Re: Bio-SamTools and Gbrowse1.7

2009-11-10T15:50:46Z

Scott Cain wrote:
> Hi Wes,
>
> Attached are the two conf files that I used to create the poster for
> GBrowse 1.70 (I think I really used 1.71b from svn, but that shouldn't
> matter, but you do need to get Bio-DB-Sam from svn). Let me know if
> you have any questions.

Hi Scott,

I am also using GBrowse 1.71b. I have built samtools-0.1.6 (without
the curses or zlib libraries because I am not trying to use it to
create .bam files or to use the samtools tview option). I just did
an svn checkout of Bio-Samtools and built and installed that. Here
are portions of my .conf file:

[GENERAL]
description = MrsFast
db_adaptor = Bio::DB::Sam
db_args = -bam /work/bs/tmp/hmgu_080725_HWI-EAS186_307FYAAXX_1.sorted.bam

[Match]
feature = match
glyph = segments
bgcolor = blue
fgcolor = blue
height = 3
label = sub {shift->display_name}
label density = 50
bump = fast
key = BAM Alignments

[CoverageXyplot]
feature = coverage:10000
glyph = wiggle_xyplot
height = 50
fgcolor = black
bicolor_pivot = 20
pos_color = blue
neg_color = red
key = XY plot
label = 0 # Labels on wiggle tracks are redundant.

The "Match" stanza works. I can see the individual reads displayed
in GBrowse. However, the coverage plot shows an empty xy plot in
GBrowse. There are no errors in my apache error log file.

What else could I be missing?

> Scott
>
>
> On Mon, Nov 9, 2009 at 11:05 PM, Wes Barris <wes.barris@...> wrote:
>> Hi,
>>
>> This poster (http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf)
>> suggests that Gbrowse 1.7 can be used to display coverage density
>> and XY plots from .bam (SamTools) files.
>>
>> I am familiar with samtools. I have .bam files and have created
>> a gbrowse .conf file using the Bio::DB::Sam adaptor. I can successfully
>> display the individual reads using a stanza that includes:
>>
>> feature = match
>> glyph = segments
>>
>> My question is: "How can I display coverage density and XY plots
>> from the .bam file?" I found the following stanza in a previous
>> post but I don't have an explanation of the "feature" or "database"
>> lines:
>>
>> [Derived1CoverageXyplot]
>> feature = coverage:2000
>> glyph = wiggle_xyplot
>> database = ecolisam
>> height = 50
>> fgcolor = black
>> bicolor_pivot = 20
>> pos_color = blue
>> neg_color = red
>> key = Derived1 coverage (xyplot)
>> label = 0 # Labels on wiggle tracks are redundant.
>>
>> Can someone provide me with a sample stanza for gbrowse 1.7?
>> --
>> Wes Barris <wes.barris@...>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
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>>
>
>
>

Upgrading Gbrowse2

2009-11-10T15:49:35Z

Hello,

I want to upgrade my Gbrowse 1.996 to 1.997 , but I've some files with
modifications like gliphs and style sheets.. will they be lost if I
upgrade? Which is the best option to upgrade it ?

Kind reggards

Miquel Ràmia

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DNA sequence callback

2009-11-10T15:46:48Z

Hi,

I'm trying to show the reference nucleotide sequence for some features
in a balloon popup. I've tryed with a callback using:

$self = shift;
$refseq = $self->dna;

but it's not working, how can I do it ?

thank you very much

Miquel Ramia

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Re: GBrowse v2 and one configuration with more databases

2009-11-10T14:24:44Z

Just based on this limited information my guess is that you have an index problem somewhere. It
sounds to me like MySQL is performing a table scan instead of using an index. Thus, when there are
lots of records in a table it is slow and it speeds up considerably when you reduce the number of
records.

You should switch back to the single database setup, perform whatever action you are doing to test
the speed of GBrowse and then execute a "show full processlist;" command on your mysql server to see
what the slow query or queries are. You can then start using EXPLAIN commands with the slow queries
to make sure that all queries are using indices when possible.

Josh

Dave Clements, GMOD Help Desk wrote:

> Hi Alessandra,
>
> Thanks for the reminder on this unanswered email. My comments are inline below.
>
>> I have got more tracks: simple match type about short reads, more
>> xyplot type, some wiggle_xyplot type, more segments.. for a total:
>> 1) if I manage all records in one database, 19G
>> 2) if I manage records in 15 databases, 15G splitted in ~1G for each database
>>
>> With first methods, GBrowse runs but it is very slowly.
>> With second methods, GBrowse runs and it is very fastly (I'm very happy!!!)
>
> That strikes me as strange, but I'm not a MySQL guru either. I'm
> going to guess that all of this speedup comes from MySQL, rather than
> GBrowse (others may correct me on that). Are these 15 different
> databases in one MySQL server, or are there multiple MySQL servers
> involved?
>
>> Second configuration has a big problem: after some request, I have got
>> 500 error system.
>> Mysql didn't cater to requests but if I kill all GBrowse process, then
>> Mysql begins again to carter to requests.
>> With Phpmyadmin Version 3.2.2, I observed Mysql returns warning about
>> some parameters:
>>
>> Handler_read_rnd: 2,378
>> [remember: this number is big when more queries request data ordering
>> or when joins use keys not correct]
>> Handler_read_rnd_next:26 k
>> [remember: generally if it is big, then tables are not correct
>> index-link or queries wrote without using index-link]
>> Select_full_join: 2
>> [remember: number of joins that they didn't use index-link]
>> Opened_tables: 2,892
>> [remember: if it is big, maybe table cache is more little]
>> Table_locks_waited: 7
>> [remember: if this number is big, maybe problems about queries optimizing]
>
> Having 15 separate databases instead of one will increase your
> connections, open databases, and open tables by 15x. I would not
> think it would affect your overall need for cache. Increasing
> table_cache (max # of open tables for all threads - and this param is
> deprecated in most recent releases) might be the right solution here.
> You may also want to check max_connections, max_user_connections.
>
>> Well, I could increase in size about 'table cache' parameter but I think that:
>> 1) I make a mistake about my configuration files (files attached)
>> 2) and/or there are serious problems about tables index-link
>> 3) and/or there are keys not correct about joins
>> 4) and/or there are queries wrote without using index-link
>>
>> Can you help me about refine configuration file?
>> The problem is mine or points like 2,3 or 4 are there true?
>
> I favor the table cache explanation, until we have a reason to think
> that is not it. Issues 2,3 and 4 would be the same with 1 database or
> 15 databases.
>
> Dave C.
>> Best,
>> Alessandra.
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry® Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9-12, 2009. Register now!
>> http://p.sf.net/sfu/devconf
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>

Re: GBrowse v2 and one configuration with more databases

2009-11-10T13:20:55Z

Hi Alessandra,

Thanks for the reminder on this unanswered email. My comments are inline below.

> I have got more tracks: simple match type about short reads, more
> xyplot type, some wiggle_xyplot type, more segments.. for a total:
> 1) if I manage all records in one database, 19G
> 2) if I manage records in 15 databases, 15G splitted in ~1G for each database
>
> With first methods, GBrowse runs but it is very slowly.
> With second methods, GBrowse runs and it is very fastly (I'm very happy!!!)

That strikes me as strange, but I'm not a MySQL guru either. I'm
going to guess that all of this speedup comes from MySQL, rather than
GBrowse (others may correct me on that). Are these 15 different
databases in one MySQL server, or are there multiple MySQL servers
involved?

> Second configuration has a big problem: after some request, I have got
> 500 error system.
> Mysql didn't cater to requests but if I kill all GBrowse process, then
> Mysql begins again to carter to requests.
> With Phpmyadmin Version 3.2.2, I observed Mysql returns warning about
> some parameters:
>
> Handler_read_rnd: 2,378
> [remember: this number is big when more queries request data ordering
> or when joins use keys not correct]
> Handler_read_rnd_next:26 k
> [remember: generally if it is big, then tables are not correct
> index-link or queries wrote without using index-link]
> Select_full_join: 2
> [remember: number of joins that they didn't use index-link]
> Opened_tables: 2,892
> [remember: if it is big, maybe table cache is more little]
> Table_locks_waited: 7
> [remember: if this number is big, maybe problems about queries optimizing]

Having 15 separate databases instead of one will increase your
connections, open databases, and open tables by 15x. I would not
think it would affect your overall need for cache. Increasing
table_cache (max # of open tables for all threads - and this param is
deprecated in most recent releases) might be the right solution here.
You may also want to check max_connections, max_user_connections.

>
> Well, I could increase in size about 'table cache' parameter but I think that:
> 1) I make a mistake about my configuration files (files attached)
> 2) and/or there are serious problems about tables index-link
> 3) and/or there are keys not correct about joins
> 4) and/or there are queries wrote without using index-link
>
> Can you help me about refine configuration file?
> The problem is mine or points like 2,3 or 4 are there true?

I favor the table cache explanation, until we have a reason to think
that is not it. Issues 2,3 and 4 would be the same with 1 database or
15 databases.

Dave C.

>
> Best,
> Alessandra.
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9-12, 2009. Register now!
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>