Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-11-01 Thread Andreas Kuntzagk

Hi,

thank you for the pointer.
I was only looking at this wiki page:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

Maybe this should point to your page?

regards, Andreas

On 31.10.2012 17:50, Carlos Borroto wrote:

On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:

Hi,

I'm still setting up a local galaxy. Currently I'm testing the setup of NGS
tools. If I try SAM to BAM for a BAM file that has hg18 set as build I
get a message that
Sequences are not currently available for the specified build. I guess
that I have either to manipulate one of the .loc files (but which?) or have
to download additional data from rsync server.
(I already have the tool-data/shared/hg18 completely)



The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'.
You can find information about this subject in the wiki[1]. Although
the table there is not complete, so you could always find the right
xml under 'tools' and poke inside to find a line like this one:
validator type=dataset_metadata_in_file
filename=sam_fa_indices.loc metadata_name=dbkey
metadata_column=1 message=Sequences are not currently available for
the specified build. line_startswith=index /

[1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

And I agree, dealing with .loc files is quite cumbersome.

Hope it helps,
Carlos



--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-11-01 Thread Carlos Borroto
Well is not my page, I'm not directly related to Galaxy. Still, I
think Galaxy Project would be happy to receive updates to the wiki,
maybe a complete table can be added to the page you are mentioning.

On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:
 Hi,

 thank you for the pointer.
 I was only looking at this wiki page:
 http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

 Maybe this should point to your page?

 regards, Andreas


 On 31.10.2012 17:50, Carlos Borroto wrote:

 On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
 andreas.kuntz...@mdc-berlin.de wrote:

 Hi,

 I'm still setting up a local galaxy. Currently I'm testing the setup of
 NGS
 tools. If I try SAM to BAM for a BAM file that has hg18 set as build
 I
 get a message that
 Sequences are not currently available for the specified build. I guess
 that I have either to manipulate one of the .loc files (but which?) or
 have
 to download additional data from rsync server.
 (I already have the tool-data/shared/hg18 completely)


 The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'.
 You can find information about this subject in the wiki[1]. Although
 the table there is not complete, so you could always find the right
 xml under 'tools' and poke inside to find a line like this one:
 validator type=dataset_metadata_in_file
 filename=sam_fa_indices.loc metadata_name=dbkey
 metadata_column=1 message=Sequences are not currently available for
 the specified build. line_startswith=index /

 [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

 And I agree, dealing with .loc files is quite cumbersome.

 Hope it helps,
 Carlos


 --
 Andreas Kuntzagk

 SystemAdministrator

 Berlin Institute for Medical Systems Biology at the
 Max-Delbrueck-Center for Molecular Medicine
 Robert-Roessle-Str. 10, 13125 Berlin, Germany

 http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-11-01 Thread Andreas Kuntzagk

Sorry for my unclear sentence, I meant the page you pointed me too.

regards, Andreas

On 01.11.2012 14:50, Carlos Borroto wrote:

Well is not my page, I'm not directly related to Galaxy. Still, I
think Galaxy Project would be happy to receive updates to the wiki,
maybe a complete table can be added to the page you are mentioning.

On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:

Hi,

thank you for the pointer.
I was only looking at this wiki page:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

Maybe this should point to your page?

regards, Andreas


On 31.10.2012 17:50, Carlos Borroto wrote:


On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:


Hi,

I'm still setting up a local galaxy. Currently I'm testing the setup of
NGS
tools. If I try SAM to BAM for a BAM file that has hg18 set as build
I
get a message that
Sequences are not currently available for the specified build. I guess
that I have either to manipulate one of the .loc files (but which?) or
have
to download additional data from rsync server.
(I already have the tool-data/shared/hg18 completely)



The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'.
You can find information about this subject in the wiki[1]. Although
the table there is not complete, so you could always find the right
xml under 'tools' and poke inside to find a line like this one:
validator type=dataset_metadata_in_file
filename=sam_fa_indices.loc metadata_name=dbkey
metadata_column=1 message=Sequences are not currently available for
the specified build. line_startswith=index /

[1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

And I agree, dealing with .loc files is quite cumbersome.

Hope it helps,
Carlos



--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich


--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/


[galaxy-dev] which .loc file for SAM to BAM?

2012-10-31 Thread Andreas Kuntzagk

Hi,

I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try SAM to 
BAM for a BAM file that has hg18 set as build I get a message that
Sequences are not currently available for the specified build. I guess that I have either to 
manipulate one of the .loc files (but which?) or have to download additional data from rsync server.

(I already have the tool-data/shared/hg18 completely)

regards, Andreas

Btw. Do you have any plans to ease the pain on adding additional builds? Something simpler than 
having to add one line for each build*tool combo? These lines seem very redundant to me.


--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-10-31 Thread Carlos Borroto
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:
 Hi,

 I'm still setting up a local galaxy. Currently I'm testing the setup of NGS
 tools. If I try SAM to BAM for a BAM file that has hg18 set as build I
 get a message that
 Sequences are not currently available for the specified build. I guess
 that I have either to manipulate one of the .loc files (but which?) or have
 to download additional data from rsync server.
 (I already have the tool-data/shared/hg18 completely)


The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'.
You can find information about this subject in the wiki[1]. Although
the table there is not complete, so you could always find the right
xml under 'tools' and poke inside to find a line like this one:
validator type=dataset_metadata_in_file
filename=sam_fa_indices.loc metadata_name=dbkey
metadata_column=1 message=Sequences are not currently available for
the specified build. line_startswith=index /

[1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

And I agree, dealing with .loc files is quite cumbersome.

Hope it helps,
Carlos
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in your mail client.  To manage your subscriptions to this
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