GBrowse Syn (At once use the more track from two database)

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GBrowse Syn (At once use the more track from two database)

Hyunmin Kim
Hi, all

I set the GBrowse sun database.

and I wonder how can I hand the two database in GBrowse sun config file.

For example, I can handle two database with below config in general gbrowse .
but this is not work in GBrowse syn config.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1_annotation
#search options = default +autocomplete

Thanks,

Hyunmin

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Re: GBrowse Syn (At once use the more track from two database)

Sheldon McKay
Hi Hyunmin,

Sorry, gbrowse_syn uses a simpler configuration that does not support multiple databases for a single species.

Sheldon McKay


On Mon, May 26, 2014 at 9:16 PM, Hyunmin Kim <[hidden email]> wrote:
Hi, all

I set the GBrowse sun database.

and I wonder how can I hand the two database in GBrowse sun config file.

For example, I can handle two database with below config in general gbrowse .
but this is not work in GBrowse syn config.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1_annotation
#search options = default +autocomplete

Thanks,

Hyunmin

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Test it for FREE on our Cloud platform anytime!
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Re: GBrowse Syn (At once use the more track from two database)

Hyunmin Kim
Thanks for your reply.

I checked it.

Hyunmin

2014. 5. 27., 오후 9:41, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

Sorry, gbrowse_syn uses a simpler configuration that does not support multiple databases for a single species.

Sheldon McKay


On Mon, May 26, 2014 at 9:16 PM, Hyunmin Kim <[hidden email]> wrote:
Hi, all

I set the GBrowse sun database.

and I wonder how can I hand the two database in GBrowse sun config file.

For example, I can handle two database with below config in general gbrowse .
but this is not work in GBrowse syn config.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1_annotation
#search options = default +autocomplete

Thanks,

Hyunmin

------------------------------------------------------------------------------
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Our experts will assist you in its installation for $59/mo, no commitment.
Test it for FREE on our Cloud platform anytime!
http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk
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Re: GBrowse Syn (At once use the more track from two database)

Hyunmin Kim
and I have another question.

####

Sorry: the size of region scaffold109:12454..2570552 exceeds the maximum (2 Mbp)


###

Can I solve this issue?

Thanks,

Hyunmin

2014. 5. 27., 오후 11:40, Hyunmin Kim <[hidden email]> 작성:

Thanks for your reply.

I checked it.

Hyunmin

2014. 5. 27., 오후 9:41, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

Sorry, gbrowse_syn uses a simpler configuration that does not support multiple databases for a single species.

Sheldon McKay


On Mon, May 26, 2014 at 9:16 PM, Hyunmin Kim <[hidden email]> wrote:
Hi, all

I set the GBrowse sun database.

and I wonder how can I hand the two database in GBrowse sun config file.

For example, I can handle two database with below config in general gbrowse .
but this is not work in GBrowse syn config.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1_annotation
#search options = default +autocomplete

Thanks,

Hyunmin

------------------------------------------------------------------------------
The best possible search technologies are now affordable for all companies.
Download your FREE open source Enterprise Search Engine today!
Our experts will assist you in its installation for $59/mo, no commitment.
Test it for FREE on our Cloud platform anytime!
http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




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The best possible search technologies are now affordable for all companies.
Download your FREE open source Enterprise Search Engine today!
Our experts will assist you in its installation for $59/mo, no commitment.
Test it for FREE on our Cloud platform anytime!
http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk
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Re: GBrowse Syn (At once use the more track from two database)

Sheldon McKay
Hi Hyunmin,

The maximum allowed segment for display is a configurable option ('max_segment' in the *.synconf file).  The default value is 2 Mbase.  I do not recommend much more than that unless your data are fairly sparse or simple.

Sheldon



On Tue, May 27, 2014 at 10:46 AM, Hyunmin Kim <[hidden email]> wrote:
and I have another question.

####

Sorry: the size of region scaffold109:12454..2570552 exceeds the maximum (2 Mbp)


###

Can I solve this issue?

Thanks,

Hyunmin

2014. 5. 27., 오후 11:40, Hyunmin Kim <[hidden email]> 작성:

Thanks for your reply.

I checked it.

Hyunmin

2014. 5. 27., 오후 9:41, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

Sorry, gbrowse_syn uses a simpler configuration that does not support multiple databases for a single species.

Sheldon McKay


On Mon, May 26, 2014 at 9:16 PM, Hyunmin Kim <[hidden email]> wrote:
Hi, all

I set the GBrowse sun database.

and I wonder how can I hand the two database in GBrowse sun config file.

For example, I can handle two database with below config in general gbrowse .
but this is not work in GBrowse syn config.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn koref_1_annotation
#search options = default +autocomplete

Thanks,

Hyunmin

------------------------------------------------------------------------------
The best possible search technologies are now affordable for all companies.
Download your FREE open source Enterprise Search Engine today!
Our experts will assist you in its installation for $59/mo, no commitment.
Test it for FREE on our Cloud platform anytime!
http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse





------------------------------------------------------------------------------
The best possible search technologies are now affordable for all companies.
Download your FREE open source Enterprise Search Engine today!
Our experts will assist you in its installation for $59/mo, no commitment.
Test it for FREE on our Cloud platform anytime!
http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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