[galaxy-user] Tophat version

Hi, Just wondering when the tophat portion of Galaxy will be updated? Its currently version 1.1.1 and there is now a version 1.2.0 (in fact I think there have been 4 updates). Cheers David ___ The Galaxy User list should be used for the

[galaxy-user] A genbank to gtf converter

Hi again, Does anyone know of a genbank to gtf converter? I have heard such things exist but never found one... Cheers David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public se

[galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

Hello, I have been able to get Galaxy to instantiate on our Cloud account, and would like to use the NGS tools to trim and map Illumina libraries. However, when I tried to import .txt files (the data contained in these files are in fastq format) located in an S3 bucket, Galaxy did not recognize

Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

Hi Karl, As a quick check, are the permissions for the S3 file set so anyone can read the file? That's required before Galaxy's upload tool will be able to access the file. Alternatively, if you don't want to set such loose permissions, you should be able to get a a signed URL for the given file us

Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

Karl, For the URL you're pasting, is it the full path to a file in your s3 bucket, including the protocol (http://) ? For galaxy to recognize that it needs to pull from a URL rather than the contents of the box, you need to use the full string. -Dannon On Mar 14, 2011, at 4:40 PM, karlerh...

Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

Ah, permissions, that may be the ticket. I will try again and see. thanks a lot! karl > Hi Karl, > As a quick check, are the permissions for the S3 file set so anyone can > read > the file? That's required before Galaxy's upload tool will be able to > access > the file. > Alternatively, if yo

Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

I changed the permission for the files to public (everyone can open/download), but this did not fix the problem. Also, to answer Dannon's question, I am entering the full path for these files, eg. https://s3.amazonaws.com/bucketname/xyz.txt >From the screencasts I have watched, I noticed that fa

Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

Hi Karl, Using the upload tool for https URLs was added in changeset 5220:425076fe5ea0. I am not sure when this will make it to the Cloud image, but meanwhile, if you can access the file without using ssl (just 'http'), you should be able to upload. If this is not the issue you are experiencing