Hi jen, I just finished FTP of R4 data set with 8.4 GB. Why can't I see the data on the right panel of galaxy after loggin in?
Tao
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, August 09, 2011 3:26 PM To: Peng, Tao Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data
Hello Tao,
It sounds like the load works with an uncompressed file but is failing when compressed? Perhaps there is a problem with the compression itself.
We can't really help with this part of the process except to note which compression types we accept. The help wiki link again is: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP
The final goal would be to have all of the data compressed and then load
using FTP in a batch. If this takes too long to run, then the next option is to run either a local or cloud install. Help can be found at: http://getgalaxy.org http://galaxyproject.org/Admin/Cloud
Please send all questions related to local or cloud installations to
Hi Jen, I have RNA-seq data for 2 biologial samples loaded in to galaxy. The samples are from human skin biopsies from genital herpes reactivation. Using Tophat I will align the reads to human genome. But I am NOT how to build genital herpes genome (HSV-2) and aligh reads to HSV-2 genome? Any suggestion is greatly appreciated! Thanks, tao -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 12, 2011 11:54 AM To: Peng, Tao; galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data Hello, Glad to hear that you were able to load your data. When logged in, FTP loaded data will initially be in the FTP upload area under the "Get Data -> Upload" tool (in the center pane). From here, load data into the history that you wish to work with. If you are not sure where this is exactly, please note the graphics in the FTP wiki and screencast. As a reminder, please send all new and followup questions with a to or cc to the mailing list, not to individual team members. This is important for our team to be able to track and answer questions. We would appreciate your helping out with this going forward. Hopefully this helps. Jen Galaxy team On 8/12/11 11:39 AM, Peng, Tao wrote: the
galaxy-dev@bx.psu.edu mailing list and not to individual team members
or
to the galaxy-bugs@bs.psu.edu mailing list.
Best wishes for your project,
Jen Galaxy team
On 8/9/11 2:25 PM, Peng, Tao wrote:
If I up-load one file (uncompressed) at one time, I will have 4x8=32 files to up-load. Each file takes about 1 hour to load. This is untenable. Any suggestion?
Thanks,
tao
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, August 09, 2011 2:04 PM To: Peng, Tao; galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data
On 8/9/11 1:55 PM, Peng, Tao wrote:
Hi Jen, if I have 8 fastq.gz files for each of my 4 samples, how should I load the data for analysis in galaxy?
Thanks,
tao
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, August 09, 2011 1:31 PM To: Peng, Tao Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data
Hello Tao,
For your other question sent to me directly, Galaxy will accept only one
file per archive, so sending a multi-file .gz will result in only
the
first file in the archive loaded into the "Get Data -> Upload" FTP area.
Given the current issues, please try a restart. Log out of Galaxy and FileZilla (and restart your computer if possible). Then begin again, testing with a single, uncompressed file. You do not have to be logged into your Galaxy account to load with FileZilla, but you will need to be
logged in to access the files on the "Get Data -> Upload" form after upload is complete.
If this fails, perhaps try reinstalling FileZilla or even a different FTP client. This tutorial covers an alternative that can also be used from the desktop: http://galaxyproject.org/Learn/Upload via FTP
If you do have more questions, please leave galaxy-bugs@bx.psu.edu on the cc list so that our entire team can help contribute to replies. This
may also be a question that you want to ask the larger user community at
galaxy-user@bx.psu.edu, as this sounds like an external issue. Another user may have encountered this problem using a PC and have suggestions.
Thanks!
Jen Galaxy team
Hi jen, I attached a screen shot of FileZilla. Do you know why the top panel says "disconnected from server" while the bottom panel indicates it is transferring the data?
Thanks,
tao
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Monday, August 08, 2011 4:55 PM To: Peng, Tao Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data
Hello Tao,
The loading times do seem to be long for the size of the files,
the internet connection is the problem. That said, FileZilla can restart
an FTP if it is interrupted and a message would be reported. I didn't see any restarts reported in the log in the screenshot you sent.
The compression is another place to look for a problem. You might
On 8/9/11 1:16 PM, Peng, Tao wrote: perhaps try to
use an alternate compression or no compression and load that way.
Try
one file, through FileZilla, as a test to see if that performs better. Winzip can compress in a few different formats, .bz2 is also accepted by
Galaxy.
Hopefully one of these will work. Please keep galaxy-bugs in the cc for any follow-up so that our team can help contribute to replies,
Thanks,
Jen
On 8/8/11 4:04 PM, Peng, Tao wrote:
Hi jen, when I FTP 9 of the fasq.gz files (each about 350 MB) for sample, the FTP program (FileZilla) keep coping the files again and again, this is strange to me. Do you know what went wrong here.
I attached a powerpoint slide that is the screen shot of FileZila (R1_002.fasq.gz has been copied 3x so far??)
Thanks,
tao
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, July 29, 2011 1:20 PM To: Peng, Tao Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data
Hello Tao,
Our apologies, the public Galaxy instance at http://usegalaxy.org has been experiencing higher than usual usage the last few days. This should
now be improved. Please try your FTP load again - it is the best way to load files and the sizes you mention are well within the accepted limits.
Thank you for your patience,
Best,
Jen Galaxy team
On 7/29/11 9:47 AM, Peng, Tao wrote:
Hi I work at FHCRC in Seattle. I am trying to load the FASQ data from Illumina HySeq. I have 4 samples with 2.4 GB of seq data per sample. For the overnight FTP, I can't even finish loading half of one sample. Is there any faster way to load the data? Can GALAXY do the analysis for this type of large data?
Thanks,
tao
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support