Galaxy on the cloud requests
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
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 < p.martin.samuel.rao@gmail.com> 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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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
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 <chapmanb@50mail.com> 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
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 <eafgan@emory.edu> 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 <chapmanb@50mail.com> 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
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
participants (3)
-
Brad Chapman -
Enis Afgan -
Martin Paradesi