Galaxy on the cloud requests

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Galaxy on the cloud requests

Martin Paradesi
Hi Galaxy team,

   I am using Galaxy on the cloud and noticed that a genome index and few tools were missing. More specifically, I noticed that bwa cannot be aligned with hg18 and rmdup and view commands are not available in the SAMTools. Do you have any plans for adding these in the near future?

Thanks,
Martin

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Re: Galaxy on the cloud requests

Enis Afgan-2
Hi Martin, 
We don't have a definitive plan for adding the specific functionality you asked about to the cloud but now that you have requested it, we can definitely look into it. In the near future (i.e., next couple of weeks), we'll be rolling out an updated version of Galaxy Cloud so we can try to provide support for your scenario then as well.
Let us know if you find something else missing so we can bunch it all up at once.

Enis

On Thu, Jun 24, 2010 at 3:49 PM, Martin Paradesi <[hidden email]> wrote:
Hi Galaxy team,

   I am using Galaxy on the cloud and noticed that a genome index and few tools were missing. More specifically, I noticed that bwa cannot be aligned with hg18 and rmdup and view commands are not available in the SAMTools. Do you have any plans for adding these in the near future?

Thanks,
Martin

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Re: Galaxy on the cloud requests

Brad Chapman
Enis and Martin;

> >    I am using Galaxy on the cloud and noticed that a genome index and few
> > tools were missing. More specifically, I noticed that bwa cannot be aligned
> > with hg18 and rmdup and view commands are not available in the SAMTools. Do
> > you have any plans for adding these in the near future?

> We don't have a definitive plan for adding the specific functionality you
> asked about to the cloud but now that you have requested it, we can
> definitely look into it. In the near future (i.e., next couple of weeks),

This weekend I did some work towards trying to help with this sort
of thing. This is a publicly available EBS snapshot with several
common genomes (including hg18) indexed for bwa,  bowtie, maq and
twobit:

snap-67446d0f

This also includes a galaxy directory with the .loc files indexed
appropriately if you mount it as /vol/galaxy on an Amazon share; to
give you an idea of the automated approach I was hoping to take
towards aligning it with Galaxy.

There are also two new Cloud BioLinux AMIs that include bwa,
bowtie, samtools and lots of other stuff:

64bit: ami-d62cc4bf
32bit: ami-5423cb3d

Enis, I'm planning to add other genomes based on what y'all have on
the public galaxy and am happy to have you guys using whatever is
useful from this. I'm hoping to write up docs and something more
official and we can discuss in a couple of weeks in Boston,

Brad
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Re: Galaxy on the cloud requests

Enis Afgan-2
Maybe it would be a good idea then if we made some sort of a 'standard distribution' for desirable genomes and agreed on where they get put on an EBS volume to be able to piggyback off of each other?
Discussing it at the meeting sounds great...

See you then,
Enis

On Thu, Jun 24, 2010 at 4:53 PM, Brad Chapman <[hidden email]> wrote:
Enis and Martin;

> >    I am using Galaxy on the cloud and noticed that a genome index and few
> > tools were missing. More specifically, I noticed that bwa cannot be aligned
> > with hg18 and rmdup and view commands are not available in the SAMTools. Do
> > you have any plans for adding these in the near future?

> We don't have a definitive plan for adding the specific functionality you
> asked about to the cloud but now that you have requested it, we can
> definitely look into it. In the near future (i.e., next couple of weeks),

This weekend I did some work towards trying to help with this sort
of thing. This is a publicly available EBS snapshot with several
common genomes (including hg18) indexed for bwa,  bowtie, maq and
twobit:

snap-67446d0f

This also includes a galaxy directory with the .loc files indexed
appropriately if you mount it as /vol/galaxy on an Amazon share; to
give you an idea of the automated approach I was hoping to take
towards aligning it with Galaxy.

There are also two new Cloud BioLinux AMIs that include bwa,
bowtie, samtools and lots of other stuff:

64bit: ami-d62cc4bf
32bit: ami-5423cb3d

Enis, I'm planning to add other genomes based on what y'all have on
the public galaxy and am happy to have you guys using whatever is
useful from this. I'm hoping to write up docs and something more
official and we can discuss in a couple of weeks in Boston,

Brad


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Re: Galaxy on the cloud requests

Martin Paradesi
Enis & Brad,

   I will prepare a list of tools and indices that are used frequently here and we can discuss about the standard distribution at Boston.

See you guys there,
Martin

On Thu, Jun 24, 2010 at 5:22 PM, Enis Afgan <[hidden email]> wrote:
Maybe it would be a good idea then if we made some sort of a 'standard distribution' for desirable genomes and agreed on where they get put on an EBS volume to be able to piggyback off of each other?
Discussing it at the meeting sounds great...

See you then,
Enis

On Thu, Jun 24, 2010 at 4:53 PM, Brad Chapman <[hidden email]> wrote:
Enis and Martin;

> >    I am using Galaxy on the cloud and noticed that a genome index and few
> > tools were missing. More specifically, I noticed that bwa cannot be aligned
> > with hg18 and rmdup and view commands are not available in the SAMTools. Do
> > you have any plans for adding these in the near future?

> We don't have a definitive plan for adding the specific functionality you
> asked about to the cloud but now that you have requested it, we can
> definitely look into it. In the near future (i.e., next couple of weeks),

This weekend I did some work towards trying to help with this sort
of thing. This is a publicly available EBS snapshot with several
common genomes (including hg18) indexed for bwa,  bowtie, maq and
twobit:

snap-67446d0f

This also includes a galaxy directory with the .loc files indexed
appropriately if you mount it as /vol/galaxy on an Amazon share; to
give you an idea of the automated approach I was hoping to take
towards aligning it with Galaxy.

There are also two new Cloud BioLinux AMIs that include bwa,
bowtie, samtools and lots of other stuff:

64bit: ami-d62cc4bf
32bit: ami-5423cb3d

Enis, I'm planning to add other genomes based on what y'all have on
the public galaxy and am happy to have you guys using whatever is
useful from this. I'm hoping to write up docs and something more
official and we can discuss in a couple of weeks in Boston,

Brad



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Re: Galaxy on the cloud requests

Brad Chapman
Martin and Enis;

> > Maybe it would be a good idea then if we made some sort of a 'standard
> > distribution' for desirable genomes and agreed on where they get put on an
> > EBS volume to be able to piggyback off of each other?
> > Discussing it at the meeting sounds great...
[...]
>    I will prepare a list of tools and indices that are used frequently here
> and we can discuss about the standard distribution at Boston.

This sounds great. A community effort to establish a standard
distribution would be perfect. So far I've been using an automated
Fabric script:

http://github.com/chapmanb/bcbb/blob/master/galaxy/galaxy_fabfile.py

to do the builds which should make it easy to add new genomes and
indexes. Let us know what would be most useful and we'll put it
together.

Looking forward to talking more in Boston,
Brad

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