question from a new Galaxy user
[NOTE: I SENT THIS SAME MESSAGE FROM A DIFFERENT EMAIL SERVER NOT CORRESPONDING TO MY USER EMAIL ADDRESS, SO THIS IS A REPEAT EMAIL] Hello: I apologize for bothering you but I am just beginning to work with mRNAseq data and it appears as though Galaxy will be quite useful but I suspect, even after looking some of the tutorials that I will be either making mistakes or just not have a good sense of things. I used "Fetch" off a new Mac computer to ftp 2 datasets yesterday whose sum total memory was over 26gb. It took 5 and one half hours to do that (my login is elwood.linney@duke.edu). This morning I had hoped to align this fastq data using your tools. When I identified the two files to put them in the right, history column of galaxy, it appears as though this transfer is taking a long time. Could you give me a time expectation of how long it might take to transfer say a 13gb file into the program if it has already been ftp'd to your site? The unspoken question above is "am I doing something wrong". Sincerely, but naively, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center
Hello Elwood, Just to double check (although you have probably already seen it), when using the FTP client, the same basic steps from this wiki were followed? Also please that you can FTP compressed data: http://wiki.g2.bx.psu.edu/FTPUpload Moving data from the FTP transfer area on the "Get Data" form into a history can take a variable amount of time. Size of the data is one factor. How busy Galaxy is is another. Galaxy has been very busy today. Please give you data some more time to complete the transfer. If the jobs times out or ends in an error, please send a bug report (click on green bug icon). Best, Jen Galaxy team On 3/7/12 7:32 AM, Elwood Linney, Ph.D. wrote:
[NOTE: I SENT THIS SAME MESSAGE FROM A DIFFERENT EMAIL SERVER NOT CORRESPONDING TO MY USER EMAIL ADDRESS, SO THIS IS A REPEAT EMAIL]
Hello: I apologize for bothering you but I am just beginning to work with mRNAseq data and it appears as though Galaxy will be quite useful but I suspect, even after looking some of the tutorials that I will be either making mistakes or just not have a good sense of things.
I used "Fetch" off a new Mac computer to ftp 2 datasets yesterday whose sum total memory was over 26gb. It took 5 and one half hours to do that (my login is elwood.linney@duke.edu). This morning I had hoped to align this fastq data using your tools. When I identified the two files to put them in the right, history column of galaxy, it appears as though this transfer is taking a long time. Could you give me a time expectation of how long it might take to transfer say a 13gb file into the program if it has already been ftp'd to your site?
The unspoken question above is "am I doing something wrong".
Sincerely, but naively,
Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center
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If I may add, I believe galaxy will uncompress your files if zipped. Unzipping a 13 GB file, will take a while. Kev
participants (3)
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Elwood Linney, Ph.D. -
Jennifer Jackson -
Kevin L