Re: [galaxy-user] File upload
Hi Scott, I am sorry that you have been having problems - and hope that I can help. I just tested FTP right now - and it is working for me. My guess is that the server name being entered is incorrect. You want this to be "usegalaxy.org" (not "usergalaxy.org") for the main public site (or be whatever the base url is for the other public servers, that are supporting FTP, you may be using). On any server, this is generally noted on the 'Upload File' tool itself, in the FTP section paragraph. This is the section for the public server: The window on this tool is only appropriate for two types of upload functions, either typing in text or entering a remote URL where data is available. This remote URL could be to a FTP server, but the process is different from loading local data (on your own computer) via FTP to the Galaxy server. The video (also linked from the wiki) for this tool demonstrates all four methods for loading data. The first method is a basic browser upload of a small file - which seems to be what you are asking about - how can I help more with this part? http://vimeo.com/galaxyproject/upload For deleting data, you can either delete individual datasets or complete histories. Which are you having trouble with? There are two videos on this wiki about datasets/histories, but it sounds like they are not covering the part you need to know. If you want to provide more details, I can try to help. https://wiki.galaxyproject.org/Learn/Managing%20Datasets The server has been problematic this week, due to circumstances out of our direct control, so if you had problems earlier, trying again is most likely a good first pass solution. You can follow our Twitter feed for updates about Main @galaxyproject - posted on our wiki here: https://wiki.galaxyproject.org/Galaxy%20on%20Twitter Usability matters, so helping you to get these operations working will probably help others as well. And I can add into our documentation what is unclear or missing. Plus most of our wiki is open - community members are encouraged to add new pages or comments to fill in/share help ideas. Thanks! Jen Galaxy team On 3/12/14 2:11 PM, Scott Tighe wrote: Jennifer It is a total mystery how to get data uploaded. Just like it is a total mystery how to delete it. Spent an hour and a half reviewing your tutorials and trying FTP. The FTP does not work anymore and if you put the term usergalaxy.org in to the FTP window, it does not like that. The tutorials were not useful and appear to be based on FTP. Maybe you could do a tutorial on how exactly to upload like 10gB. Arrggg Thanks Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) On 3/12/2014 1:17 PM, Jennifer Jackson wrote: Hi Scott, Is the 'Get Data -> Upload File' tool no longer functioning for you? Can I help with using Main or is this on a local/cloud instance that needs to be set up? https://wiki.galaxyproject.org/Support#Loading_data It is correct that the addition upload methods via the "Load Data" process - found at the top of the tool panel - are not included in our tutorials/vidoes yet. This is very new set of methods (first was placed on Main at the end of January) and may still undergo some changes. We expect this to stabilize near-term and then be documented. Both tools will continue to co-exist. If there are any usage question right now (you or others) please let us know and we can help. The functions are either the same or very similar to the 'Upload File' tool, just presented in a different pop-up interface, plus now include convenience/feedback features. Thanks! Jen Galaxy team On 3/12/14 12:57 PM, Scott Tighe wrote: For all users: The tutorial on uploading data is incorrect. I do not think they have updated "how to upload data" yet. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) -- Jennifer Hill
Re: [galaxy-user] File upload
Hi Scott, Is the 'Get Data -> Upload File' tool no longer functioning for you? Can I help with using Main or is this on a local/cloud instance that needs to be set up? https://wiki.galaxyproject.org/Support#Loading_data It is correct that the addition upload methods via the "Load Data" process - found at the top of the tool panel - are not included in our tutorials/vidoes yet. This is very new set of methods (first was placed on Main at the end of January) and may still undergo some changes. We expect this to stabilize near-term and then be documented. Both tools will continue to co-exist. If there are any usage question right now (you or others) please let us know and we can help. The functions are either the same or very similar to the 'Upload File' tool, just presented in a different pop-up interface, plus now include convenience/feedback features. Thanks! Jen Galaxy team On 3/12/14 12:57 PM, Scott Tighe wrote: For all users: The tutorial on uploading data is incorrect. I do not think they have updated "how to upload data" yet. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] file upload renamed
Hi Neil,
You're looking for the option to "link to" data, which is explained here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
--nate
On Aug 22, 2012, at 12:44 AM, wrote:
> When uploading a file using “Get Data” it seems the file is renamed to
> dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to
> keep its name rather than being renamed?
>
> It seems this is being done because of the line
>
> ${output.dataset.dataset.id}:${output.files_path}:${file_name}
>
> in the upload.xml file. But I don't know where in the code it gets
> ${file_name} from. Any ideas how i change this to get the correct name of the
> file being uploaded?
>
> Neil
>
>
> ___
> 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/
>
___
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:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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[galaxy-user] file upload renamed
When uploading a file using “Get Data” it seems the file is renamed to
dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to keep
its name rather than being renamed?
It seems this is being done because of the line
${output.dataset.dataset.id}:${output.files_path}:${file_name}
in the upload.xml file. But I don't know where in the code it gets ${file_name}
from. Any ideas how i change this to get the correct name of the file being
uploaded?
Neil
___
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/
Re: [galaxy-user] file upload
Hello Huw, To help us understand the problem, would you be able to let us know if the upload issue is while you are using Galaxy main with the FTP method (using Filezilla from a desktop or direct from a server)? Or are you using just a browser? If just a browser, please try the FTP method and see if that resolves the time lag (FTP method is explained under the same Get Data -> Upload tool). We look forward to your feedback, Best, Jen Galaxy team On 1/20/11 3:09 AM, Thomas, Huw [hbt] wrote: I have recently been attempting to upload some large data files to the galaxy portal but have had varying success. The file size range from around 1GB to around 3.5GB. On previous attempts the files of around 1GB have successfully uploaded in a matter of minutes (approx 40 mins), but I have been unable to successfully upload the largest file of 3 GB despite leaving the file in the "uploading" stage for more than 2 days, and re-attempting several times. Could you please tell me whether there is anything I can do to remedy this and in particular how long you would expect a file of around 1-3GB should take to upload to your server. Regards Huw Thomas (University of Liverpool) ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
[galaxy-user] file upload
I have recently been attempting to upload some large data files to the galaxy portal but have had varying success. The file size range from around 1GB to around 3.5GB. On previous attempts the files of around 1GB have successfully uploaded in a matter of minutes (approx 40 mins), but I have been unable to successfully upload the largest file of 3 GB despite leaving the file in the "uploading" stage for more than 2 days, and re-attempting several times. Could you please tell me whether there is anything I can do to remedy this and in particular how long you would expect a file of around 1-3GB should take to upload to your server. Regards Huw Thomas (University of Liverpool) ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
