Thank you very much for your help with this - we got that settled. One other question...we are importing sorted, indexed bam files into a galaxy data library and we are not having galaxy copy over the files (they are large) but rather just setting up galaxy such that it points to the relevant directory. We noticed that the file (160 GB in size) is taking a long time to import considering all it should be doing is creating a link. When we examined processes that are running, we noticed that samtools is running. From searching around a bit, it seems that Galaxy does this in order to groom the bam file (sort/index) and ensure that it is in the format necessary for galaxy to be able to interpret it. Is there any way around this? We did the sorting and indexing prior to import and it's taking quite a while to perform an unnecessary function. Thanks.

Greg

Dr. Gregory Miles
Bioinformatics Specialist
Cancer Institute of New Jersey @ UMDNJ
Office: (732) 235 8817

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On Mon, Apr 23, 2012 at 12:55 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Greg,

Upload your files to a Galaxy data library using a combination of "Upload files from filesystem paths" without copying data into Galaxy's default data store.

See the following wiki for all the details:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

For all of the details about data libraries, see:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries

Greg Von Kuster


On Apr 23, 2012, at 11:26 AM, Gregory Miles wrote:

> We have large files that cannot be uploaded using the "file upload" command and instead would need to be uploaded using a URL. Unfortunately, we are using a "local" install on a non-local machine, so setting up an FTP server on this machine is a security issue. The files are located on this computer already anyhow, and Galaxy would simply be copying from one folder to another in order to perform the "get data" step. Is there a simple way to have a "pointer" of some sort such that galaxy knows where this file is and:
>
> 1) Would not have to copy it and could simply refer to the file location.
> 2) Could perform data analysis steps on this file and push the output to the usual location (not the location of the data files).
>
> Any help would be greatly appreciated. Thanks.
>
> Dr. Gregory Miles
> Bioinformatics Specialist
> Cancer Institute of New Jersey @ UMDNJ
> Office: (732) 235 8817
>
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