[ezilybored]

Hi, upload limitations are going to be a problem for all of us as it is not Galaxy issue per se. To upload your files try this:
- gzip them
- put them to a web-accessible loocation
- paste a URL pointing to your files to upload tool as shown in the attached image

Aspera is incredibly expensive to license, and we're not convinced it really accelerates things that much. There are some open source alternative we will be taking a look at

Yes, blasting against custom db is on the to do list as numerous people want this to happen.

Hi there, sorry if i am being naive but will galaxy be able to read the files as gzips? a colleague of mine tried recently and said that it wasnt able to read the file format.

Ben

[nekrut]

Hi,
Also, is there a limit on how much data that I can save in my galaxy account? Thanks!

No limit as of now

[tweist]

Hi,

Have you looked at open source alternative such as UDT to address the data transfer bottleneck? Also, is there a limit on how much data that I can save in my galaxy account? Thanks!

[nekrut]

This is a great platform having many useful tools available from the same place and interoperable. However, uploading big dataset to Galaxy is a challenge and a road block. I tried to upload a ILMN dataset of a few Gb and not yet done after a day and half. Any plan to enable Aspera-like tools to accelerate the data transfer speed?

Also, I think a blast tool that allows search against arbitrary database would be useful too. Any plan to add this feature?

Great job!

Hi, upload limitations are going to be a problem for all of us as it is not Galaxy issue per se. To upload your files try this:
- gzip them
- put them to a web-accessible loocation
- paste a URL pointing to your files to upload tool as shown in the attached image

Aspera is incredibly expensive to license, and we're not convinced it really accelerates things that much. There are some open source alternative we will be taking a look at

Yes, blasting against custom db is on the to do list as numerous people want this to happen.

[tweist]

This is a great platform having many useful tools available from the same place and interoperable. However, uploading big dataset to Galaxy is a challenge and a road block. I tried to upload a ILMN dataset of a few Gb and not yet done after a day and half. Any plan to enable Aspera-like tools to accelerate the data transfer speed?

Also, I think a blast tool that allows search against arbitrary database would be useful too. Any plan to add this feature?

Great job!

[kopi-o]

Never mind, connecting worked like a charm when I followed the (presumably very recently updated) and detailed instructions at http://bitbucket.org/galaxy/galaxy-central/wiki/cloud.

This seems extremely useful!

[kopi-o]

This is great.

Just one question - is the web interface for the cloud Galaxy meant to be working? I successfully connected to the AMI and was able to log in using ssh - but I couldn't connect to the public DNS where the web interface is supposed to reside.

[nekrut]

New Quickies explaining fastq manipulation

Just added two movies explaining fastq manipulation: basic and advanced.

[nekrut]

The indexes in the manual work very well and support most types of sequence data (lengths and technologies) and genomes (long and short). Given this information, it should be trivial to get BFAST support up and running. Feel free to PM me or email me.

Great. We'll give it a shot and make a wrapper in a few weeks.

[KevinLam]

We prefer to stay on the open source side of the world = how else do you know what software actually does?

I think we can lobby for ABI to release as open source.
I mean they ain't selling the software anyway.

for ppl stuck with service providers its either you use corona lite which has very little documentation or u go with open source tools.

if no one uses ABI tools then what's the point?

[nilshomer]

Speaking of bfast, we really need Nils' input on making index generation a bit more user friendly.

I believe before, we planned to design a script that would find the "optimal" parameters for building the indexes. The indexes in the manual work very well and support most types of sequence data (lengths and technologies) and genomes (long and short). Given this information, it should be trivial to get BFAST support up and running. Feel free to PM me or email me.

[nekrut]

interesting revelation!
Galaxy: I think you should ask ABI to write wrappers for their binaries in Galaxy. I think they should be more than happy to have better support for their platform. and Bioscope is still ^%*^% propriety &^(&*^ software. This seriously limits their widespread adaptation

We prefer to stay on the open source side of the world = how else do you know what software actually does?

[KevinLam]

I guess bwa's solid support was too buggy at the time of developing galaxy. It should become better now. For solid, I think it is important to include bfast as perm/bowtie do not do gapped alignment. Bwa does gapped alignment for SOLiD, but not as good as bfast. Now I think gapped alignment is crucial to accurate variant discovery, more important than I thought before. Several other publications have already emphasized this point.

interesting revelation!
lh3: slightly OT. How would you compare bfast mapping vs bioscope's mapreads then?

Galaxy: I think you should ask ABI to write wrappers for their binaries in Galaxy. I think they should be more than happy to have better support for their platform. and Bioscope is still ^%*^% propriety &^(&*^ software. This seriously limits their widespread adaptation

[nekrut]

Are you all thinking about including other analysis tools into Galaxy like cufflinks software suite, Degseq and Eland/Erange, other R statistical packages in the near future (if so,by when?)

Cufflinks by early summer. No plans for DegSeq yet (but integrating tools into Galaxy is easy, so anyone can do this). Speaking of Eland/Erange - we give priority to Open Source tools.

[nekrut]

I guess bwa's solid support was too buggy at the time of developing galaxy. It should become better now. For solid, I think it is important to include bfast as perm/bowtie do not do gapped alignment. Bwa does gapped alignment for SOLiD, but not as good as bfast. Now I think gapped alignment is crucial to accurate variant discovery, more important than I thought before. Several other publications have already emphasized this point.

At the time the challenge was the interpretation of SAM output produced by BWA on solid reads. It will be quite simple to enable BWA for SOLiD in Galaxy, since all cs indices are alreay built. Do you think it's time to enable BWA for SOLiD again? Speaking of bfast, we really need Nils' input on making index generation a bit more user friendly.