Question: upload fastq data to galaxy in bio-linux 8
gravatar for machinemrc
4.0 years ago by
United States
machinemrc0 wrote:

I have bio-linux 8 with galaxy installed running within Virtualbox.  This is the latest version of Virtualbox is running on a MacPro.

I have fastq files with typical sizes of 3-4GB.  In the documentation I do not see any option other than uploading the data through the local server (through Get Data).  It recommends using the URL/text option for uploading the data.

I have two questions:

1. Is there an easier approach for making the files on the local drives visible to galaxy? Using a symbolic link for example?

2. If the answer to question 1 is no, what is the proper format for upload (for example, file://root-dir/path..). I hav tried this format and it does not seem to work.



rna-seq bio-linux • 1.0k views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by machinemrc0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Mach,

Using Data Libraries may be a good solution for you. Please see:

Setting up the instance to permit FTP upload is another option, or perhaps one to also include. The utility of this depends on if others will also be loading larger files or if you will want to load remote files that are not available via a URL (2G is the maximum for browser upload).

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k

Hello Jen,

thank you for the quick reply.  I thought the data library option was appropriate to my situation.  I followed the instruction in the documentation (perhaps out of date, but similar enough to follow), made the necessary modifications as best as I can determine.

I tried two different options and neither one worked.  First, I attempted the '' upload files from filesystem paths'' (the option ''upload directory of files'' was not available).  The upload file from filesystem paths option failed with an error stating that the path was not valid - the path was an absolute path copied from the command terminal.  I next tied uploading one file at a time.  This option appears to be ''hung''.  The message in the message box states that the ''dataset is uploading'', but this has been the message for the past two hours - which seems unusally long to me given my reasonably fast hardware.

This is perhaps an ''operator error'' - some parameter that I did not set correctly (although I have double checked the once described on the documentation page).

Any hint would be appreciated.




ADD REPLYlink written 4.0 years ago by machinemrc0
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