Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer

[Daniel Blankenberg]

Hi Jim,

Yes, Galaxy ships the vcf files bgzip compressed (filename.vcf.gz) and makes a 
tabix index available along side (filename.vcf.gz.tbi). In the case of Galaxy, 
the pysam package is used to create the tabix index. 


Thanks,

Dan


On Jan 17, 2012, at 9:44 AM, Jim Robinson wrote:

> Hi Dan, thanks for the response.   Does Galaxy index VCF files, for example 
> with tabix of the "tribble" library?  IGV currently requires indexes for VCF 
> files, mainly because the ones we generate here are huge.   This could be 
> relaxed for smaller VCF files, and I have that on my list.
> 
> best,
> 
> Jim
> 
>> Hi Ming,
>> 
>> From Galaxy, you can currently view BAM and VCF (VCF is available in 
>> -central, but will be in the next -dist release) files within IGV.  To do 
>> this on a local set up, you will need to have your Galaxy instance behind a 
>> proxy (e.g. nginx or apache); this enables byte-range requests. In the 
>> datatypes_conf.xml file, make sure that '' and 
>> '' are not commented out. Within Galaxy, your 
>> BAM or VCF file should have the dbkey set to a build that is configured to 
>> be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
>> 
>> Please let us know if we can provide additional assistance.
>> 
>> 
>> Thanks for using Galaxy,
>> 
>> Dan
>> 
>> 
>> On Jan 14, 2012, at 10:09 PM, bt.microzh...@gmail.com wrote:
>> 
>>> Hi Guys,
>>> I am glad to hear form Jim Robinson that  exists some code could wrap 
>>> IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant 
>>> and wanted to integrate
>>> IGV as a visualizer. I'm looking forward your reply.
>>> 
>>> Regards,
>>> 
>>> Ming 
>>> ___
>>> 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/
>> 
> 

___
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/

Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer

[Jim Robinson]

 Hi Dan, thanks for the response.   Does Galaxy index VCF files, for 
example with tabix of the "tribble" library?  IGV currently requires 
indexes for VCF files, mainly because the ones we generate here are 
huge.   This could be relaxed for smaller VCF files, and I have that on 
my list.


best,

Jim


Hi Ming,

From Galaxy, you can currently view BAM and VCF (VCF is available in 
-central, but will be in the next -dist release) files within IGV.  To 
do this on a local set up, you will need to have your Galaxy instance 
behind a proxy (e.g. nginx or apache); this enables byte-range 
requests. In the datatypes_conf.xml file, make sure that 'file="igv/bam.xml" />' and '' are not 
commented out. Within Galaxy, your BAM or VCF file should have the 
dbkey set to a build that is configured to be viewable at IGV (see 
tool-data/shared/igv/igv_build_sites.txt).


Please let us know if we can provide additional assistance.


Thanks for using Galaxy,

Dan


On Jan 14, 2012, at 10:09 PM, bt.microzh...@gmail.com 
 wrote:



Hi Guys,
I am glad to hear form Jim Robinson that  exists some code could 
wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy 
instant and wanted to integrate

IGV as a visualizer. I'm looking forward your reply.

Regards,

Ming
___
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/




___
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/

Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer

[Daniel Blankenberg]

Hi Alex,

Yes, thats the current -dist.  

I hope I don't regret saying this, but we are pushing for a new release coming 
real soon, so you may want to hold off on the update if it will require 
extensive testing on your end.


Thanks for using Galaxy,

Dan


On Jan 17, 2012, at 9:13 AM, Bossers, Alex wrote:

> Dan,
> any idea when the next dist release is scheduled? We need to upgrade our wur 
> instance seriously and from then keep up the pace, but it would be a pity if 
> we upgrade and extensively test it now, while the new release is out a few 
> days later.
> The latest is from November 18th right?!
> Thanks
> Alex
> 
> 
> 
> Van: galaxy-dev-boun...@lists.bx.psu.edu 
> [galaxy-dev-boun...@lists.bx.psu.edu] namens Daniel Blankenberg 
> [d...@bx.psu.edu]
> Verzonden: dinsdag 17 januari 2012 15:09
> Aan: igv-h...@googlegroups.com
> CC: galaxy-dev@lists.bx.psu.edu; jrobi...@broadinstitute.org
> Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a 
> Galaxy visualizer
> 
> Hi Ming,
> 
> From Galaxy, you can currently view BAM and VCF (VCF is available in 
> -central, but will be in the next -dist release) files within IGV.  To do 
> this on a local set up, you will need to have your Galaxy instance behind a 
> proxy (e.g. nginx or apache); this enables byte-range requests. In the 
> datatypes_conf.xml file, make sure that '' and 
> '' are not commented out. Within Galaxy, your 
> BAM or VCF file should have the dbkey set to a build that is configured to be 
> viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
> 
> Please let us know if we can provide additional assistance.
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 
> 
> On Jan 14, 2012, at 10:09 PM, 
> bt.microzh...@gmail.com<mailto:bt.microzh...@gmail.com> wrote:
> 
> Hi Guys,
>I am glad to hear form Jim Robinson that  exists some code could wrap IGV 
> as a Galaxy visualizer. Recently, i implemented local Galaxy instant and 
> wanted to integrate
> IGV as a visualizer. I'm looking forward your reply.
> 
> Regards,
> 
> Ming
> ___
> 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/
> 
> 
> 


___
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/

Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer

[Bossers, Alex]

Dan,
any idea when the next dist release is scheduled? We need to upgrade our wur 
instance seriously and from then keep up the pace, but it would be a pity if we 
upgrade and extensively test it now, while the new release is out a few days 
later.
The latest is from November 18th right?!
Thanks
Alex



Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
namens Daniel Blankenberg [d...@bx.psu.edu]
Verzonden: dinsdag 17 januari 2012 15:09
Aan: igv-h...@googlegroups.com
CC: galaxy-dev@lists.bx.psu.edu; jrobi...@broadinstitute.org
Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a 
Galaxy visualizer

Hi Ming,

>From Galaxy, you can currently view BAM and VCF (VCF is available in -central, 
>but will be in the next -dist release) files within IGV.  To do this on a 
>local set up, you will need to have your Galaxy instance behind a proxy (e.g. 
>nginx or apache); this enables byte-range requests. In the datatypes_conf.xml 
>file, make sure that '' and 'file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF 
>file should have the dbkey set to a build that is configured to be viewable at 
>IGV (see tool-data/shared/igv/igv_build_sites.txt).

Please let us know if we can provide additional assistance.


Thanks for using Galaxy,

Dan


On Jan 14, 2012, at 10:09 PM, 
bt.microzh...@gmail.com<mailto:bt.microzh...@gmail.com> wrote:

Hi Guys,
I am glad to hear form Jim Robinson that  exists some code could wrap IGV 
as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted 
to integrate
IGV as a visualizer. I'm looking forward your reply.

Regards,

Ming
___
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/



___
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/

Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer

[Daniel Blankenberg]

Hi Ming,

From Galaxy, you can currently view BAM and VCF (VCF is available in -central, 
but will be in the next -dist release) files within IGV.  To do this on a local 
set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx 
or apache); this enables byte-range requests. In the datatypes_conf.xml file, 
make sure that '' and '' are not commented out. Within Galaxy, your BAM or VCF 
file should have the dbkey set to a build that is configured to be viewable at 
IGV (see tool-data/shared/igv/igv_build_sites.txt).

Please let us know if we can provide additional assistance.


Thanks for using Galaxy,

Dan


On Jan 14, 2012, at 10:09 PM, bt.microzh...@gmail.com wrote:

> Hi Guys,
> I am glad to hear form Jim Robinson that  exists some code could wrap IGV 
> as a Galaxy visualizer. Recently, i implemented local Galaxy instant and 
> wanted to integrate
> IGV as a visualizer. I'm looking forward your reply.
> 
> Regards,
> 
> Ming 
> ___
> 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/

___
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/