Hi, I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time. Thanks Nan
Hello Takako, The best way to load data locally is to use the the method described here: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFile... Please let us know if we can help more, Best, Jen Galaxy team On 1/18/11 4:18 PM, Nan Deng wrote:
Hi,
I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time.
Thanks
Nan
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
-- Jennifer Jackson http://usegalaxy.org
Would it be possible to configure Galaxy to simply refuse to upload files greater than 2 GB since almost no browsers seem to support it? A large number of people seem to run into this issue. -Farhat On Wed, Jan 19, 2011 at 9:02 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Takako,
The best way to load data locally is to use the the method described here:
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFile...
Please let us know if we can help more,
Best,
Jen Galaxy team
On 1/18/11 4:18 PM, Nan Deng wrote:
Hi,
I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time.
Thanks
Nan
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
-- Jennifer Jackson http://usegalaxy.org _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Farhat, This is reasonable suggestion, I'll pass this along to the development team for consideration. Thanks for using Galaxy! Jen Galaxy team On 1/19/11 10:50 AM, Farhat Habib wrote:
Would it be possible to configure Galaxy to simply refuse to upload files greater than 2 GB since almost no browsers seem to support it? A large number of people seem to run into this issue.
-Farhat
On Wed, Jan 19, 2011 at 9:02 PM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hello Takako,
The best way to load data locally is to use the the method described here: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFile...
Please let us know if we can help more,
Best,
Jen Galaxy team
On 1/18/11 4:18 PM, Nan Deng wrote:
Hi,
I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time.
Thanks
Nan
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-user
-- Jennifer Jackson http://usegalaxy.org _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-user
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Hi Jen, If you do that, please make it an option in universe_wsgi.ini. It's fine if uploads of > 2GB will be disabled by default, but please allow me to enable it if it's working for me... Cheers, Pi On Jan 19, 2011, at 8:12 PM, Jennifer Jackson wrote:
Hi Farhat,
This is reasonable suggestion, I'll pass this along to the development team for consideration.
Thanks for using Galaxy!
Jen Galaxy team
On 1/19/11 10:50 AM, Farhat Habib wrote:
Would it be possible to configure Galaxy to simply refuse to upload files greater than 2 GB since almost no browsers seem to support it? A large number of people seem to run into this issue.
-Farhat
On Wed, Jan 19, 2011 at 9:02 PM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hello Takako,
The best way to load data locally is to use the the method described here: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFile...
Please let us know if we can help more,
Best,
Jen Galaxy team
On 1/18/11 4:18 PM, Nan Deng wrote:
Hi,
I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time.
Thanks
Nan
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-user
-- Jennifer Jackson http://usegalaxy.org _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu <mailto: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
------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online -------------------------------------------------------------
Hi Pi, Your ideas are great, too. The dev team appreciates all input and this will be passed along, too. Thanks for the feedback! Best, Jen Galaxy team On 1/20/11 1:41 AM, Pieter Neerincx wrote:
Hi Jen,
If you do that, please make it an option in universe_wsgi.ini. It's fine if uploads of> 2GB will be disabled by default, but please allow me to enable it if it's working for me...
Cheers,
Pi
On Jan 19, 2011, at 8:12 PM, Jennifer Jackson wrote:
Hi Farhat,
This is reasonable suggestion, I'll pass this along to the development team for consideration.
Thanks for using Galaxy!
Jen Galaxy team
On 1/19/11 10:50 AM, Farhat Habib wrote:
Would it be possible to configure Galaxy to simply refuse to upload files greater than 2 GB since almost no browsers seem to support it? A large number of people seem to run into this issue.
-Farhat
On Wed, Jan 19, 2011 at 9:02 PM, Jennifer Jackson<jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hello Takako,
The best way to load data locally is to use the the method described here: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFile...
Please let us know if we can help more,
Best,
Jen Galaxy team
On 1/18/11 4:18 PM, Nan Deng wrote:
Hi,
I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time.
Thanks
Nan
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu<mailto:galaxy-user@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-user
-- Jennifer Jackson http://usegalaxy.org _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu<mailto: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
------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online -------------------------------------------------------------
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
participants (4)
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Farhat Habib -
Jennifer Jackson -
Nan Deng -
Pieter Neerincx