[galaxy-user] biomart plugin

Hello If i had a local installation of galaxy is it possible to access a biomart database on my local server. It is my understanding that a dataset has to be available on the biomart central server to be accessible via the galaxy biomart plugin. thanks ___

Re: [galaxy-user] dataflow using Galaxy on Amazon EC2

Hi Luqman, Take a look a my comments below. On Fri, Mar 25, 2011 at 5:06 PM, Luqman Hodgkinson wrote: > > > > > Hi Enis, > > Thank you for your detailed reply. After playing with Galaxy, there are > some questions I have. > > 1. All my Java classes are in the same project. There is only a single

Re: [galaxy-user] dataflow using Galaxy on Amazon EC2

Hi Luqman, Were you planning on using Galaxy CloudMan (usegalaxy.org/cloud) and integrating your tool (i.e., Java classes) into the Galaxy that it deploys or simply starting a new EC2 instance and setting up a Galaxy instance from scratch? Either way, I would suggest trying the process out on your

Re: [galaxy-user] is galaxy down?

Keith, We're currently experiencing a small issue with the main galaxy server. If you could wait a while and then retry, it should be fully functional again soon. -Dannon On Mar 25, 2011, at 11:01 AM, Keith E. Giles wrote: > I keep getting a "SERVER ERROR" message. Is galaxy down, or is this

[galaxy-user] is galaxy down?

I keep getting a "SERVER ERROR" message. Is galaxy down, or is this on my end? ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on

Re: [galaxy-user] Sort & index SAM-files automatically

Hi! Thank you for your reply. So that means, I should convert the csfasta & qual to fastq, map it with Bowtie, get an SAM, convert it to BAM and then index that BAM? How can I index BAM using GALAXY? I haven´t found a way to get a BAM directly from GALAXY using csfasta & qual as input files.

Re: [galaxy-user] Sort & index SAM-files automatically

Hi Jo, To short-circuit confusion I'll jump in here. I'm the developer of IGV and igvtools, the sorting and indexing for SAM files was added long ago, even before indexed BAM files were possible from Java programs. The recommendation now is to convert to BAM and index that, although

[galaxy-user] Sort & index SAM-files automatically

Hello! I convert SOLiD csfasta- and qual-files to fastq-files and map those against Hg19 (Bowtie). I would like to use the resulting sam-files in the IGV browser (Broad Institute). Therefore, the sam-file need to be sorted an indexed. This could be done using the “igvtools”. However, it woul