Upload error in RStudio running on Amazon - AMI
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@nicholasprovart-7240
Last seen 6.5 years ago
Canada

Dear Bioconductor Support,

Thanks for setting up an instance of Bioconductor as an Amazon AMI! I've run a next-gen sequencing lab last year on Coursera.org (it was a lab within "Bioinformatic Methods II") and had students install BioC on their own laptops. This was a bit problematic, so I'd like to move to the cloud so that installation issues don't become the focus of the lab for the next run of this course starting at the end of February, 2015.

I was able to follow the tutorial to instantiate an AMI of BioC and could fire up RStudio with the provided URL. However, when I try to upload some (truncated) .fastq files of around 120 MB, I get an error of "Unexpected empty response from server" and no files are uploaded (I can upload smaller files of 100kb or so, and execute commands on these without a problem). Ideally, I'd like to provide a "canned" set of sequences for students to use of just 4 such fastq files, so I'd just like to have these in the cloud somewhere. Is there a size limit for this AMI? I couldn't find anything on the BioC support pages.

Second question: I'm aiming to have my own custom version of the BioC AMI for this new iteration of the course, and I'd like to have QuasR  (http://www.bioconductor.org/packages/release/bioc/html/QuasR.html) and ape installed (everything else seems to be present in the Bioc2.13/R3.02 AMI). Any chance of those packages being in the default AMI for that combination of BioC and R?

Thanks!

Nick

AMI RStudio upload error custom install • 1.7k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 5 months ago
United States

Hi Nick,

Thanks for using the AMI. Regarding the upload problem, it could be a size issue. Make sure there is free space. If you are starting your instance from the EC2 launch wizard, you can increase the free space in "Step 4: Add Storage". Maybe add 20GB to the 40GB shown there.

It is unlikely we will update this outdated AMI. (In fact, consider using the latest release version). But if you are going to make your own custom version, it should not be hard for you to add QuasR and ape. Let us know here if you run into any difficulties.

Thanks,
Dan

 

 

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