Enis

On Mon, Mar 14, 2011 at 11:24 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:

Hi Karl,

Using the upload tool for https URLs was added in changeset 5220:425076fe5ea0. I am not sure when this will make it to the Cloud image, but meanwhile, if you can access the file without using ssl (just 'http'), you should be able to upload. If this is not the issue you are experiencing please let us know. Do not hesitate to contact us if you need further assistance.

Thanks for using Galaxy,

Dan

On Mar 14, 2011, at 7:30 PM, karlerhard@berkeley.edu wrote:

>
> I changed the permission for the files to public (everyone can
> open/download), but this did not fix the problem.
>
> Also, to answer Dannon's question, I am entering the full path for these
> files, eg. https://s3.amazonaws.com/bucketname/xyz.txt
>
>> From the screencasts I have watched, I noticed that fastq files uploaded
> (from an S3 bucket or from elsewhere) always had a .fastq extension. Not
> sure whether this is an issue for galaxy or not.
>
>
>
>
>
>> Hi Karl,
>> As a quick check, are the permissions for the S3 file set so anyone can
>> read
>> the file? That's required before Galaxy's upload tool will be able to
>> access
>> the file.
>> Alternatively, if you don't want to set such loose permissions, you should
>> be able to get a a signed URL for the given file using a Firefox extension
>> S3Fox.
>>
>> Enis
>>
>> On Mon, Mar 14, 2011 at 4:40 PM, <karlerhard@berkeley.edu> wrote:
>>
>>>
>>> Hello,
>>>
>>> I have been able to get Galaxy to instantiate on our Cloud account, and
>>> would like to use the NGS tools to trim and map Illumina libraries.
>>>
>>> However, when I tried to import .txt files (the data contained in these
>>> files are in fastq format) located in an S3 bucket, Galaxy did not
>>> recognize them as fastq data. I tried to import the files via the URL
>>> of
>>> the S3 bucket, and Galaxy just imported the actual name of the URL
>>> rather
>>> than the file itself.
>>>
>>> Do I need to change the extension of these .txt files to .fastq? Or
>>> have
>>> I gotten something wrong with respect to the location of the data in the
>>> S3 bucket?
>>>
>>> thanks for any help!
>>>
>>> karl
>>>
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>>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/