ask for a help

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ask for a help

by liyan0316 :: Rate this Message:

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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: ask for a help

by Dave Clements, GMOD Help Desk-2 :: Rate this Message:

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Nothing stands out about the configuration file. however, it is easy to miss small problems.

A good place to start looking for what might be wrong is the Apache error log, called error.log on Windows machines. The location of that file should be specified in your Apache conf file. Try accessing your GBrowse instance and then check the log for errors that were just logged.

Dave C.

On Thu, Nov 5, 2009 at 11:42 PM, 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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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: ask for a help

by Scott Cain-4 :: Rate this Message:

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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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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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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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trial. Simplify your report design, integration and deployment - and focus on
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Re: ask for a help

by Scott Cain-4 :: Rate this Message:

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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

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