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  • cochrane
    replied
    Originally posted by GenoMax View Post
    Take a look at ENA API. I am not sure if it works with EBI SRA data but worth a try.
    Have a look at enaGroupGet at https://github.com/enasequence/enaBrowserTools - command line downloads including fastq from ENA.

    Leave a comment:


  • GenoMax
    replied
    Take a look at ENA API. I am not sure if it works with EBI SRA data but worth a try.

    Leave a comment:


  • cbmckni
    replied
    Thanks!!! @Genomax

    This kind of pointer is exactly what I was looking for. Thank you so much for your abrupt response.

    Do you have any tips on bulk downloading entire data sets from the command line?

    Here is one of such sets:



    Writing my own script is the first thing that comes to mind, but I am sure there is another way....

    Leave a comment:


  • GenoMax
    replied
    You can download fastq files directly from EBI-ENA. No need for SRAtoolkit. Example using your SRR# here.

    Leave a comment:


  • IBM Power8: Need help accessing NCBI genomes WITHOUT SRA toolkit.

    Hello everyone,

    I joined because I need help setting up a research environment on an IBM Power8 server. The tools I will be using to analyse genomes are all included in Biobuilds(which I installed without any issues), except for one. We will be using genomes stored in NCBI's repository, which requires you to install NGS/SRA toolkit to download them.

    Here is an example of a command I would need to run:

    $ fastq-dump -X 5 -Z SRR390728

    My issue is this: NGS/SRA toolkit does not offer support for the power8 architecture. I have tried normal installation and installing from source code, both of which gave me error messages along the lines of "unsupported architecture"(which is Ubuntu ppc64le).

    Does anyone know a way to download .sra files and convert them to fastq, without using the toolkit?

    I have tried a wget command I found online, but that gave me a message along the lines of "please download SRA toolkit".

    Workaround:

    If I am unable to figure this out soon, I will be forced to download and convert the data using Clemson's Palmetto Cluster, then upload the files to github, then download them to the IBM server(which is a huge waste of time and resources).

    Any advice, or simply a point in the right direction would be greatly appreciated.

    Thanks,

    Cole

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