Originally posted by nilshomer
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This is great.
Just one question - is the web interface for the cloud Galaxy meant to be working? I successfully connected to the AMI and was able to log in using ssh - but I couldn't connect to the public DNS where the web interface is supposed to reside.
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Never mind, connecting worked like a charm when I followed the (presumably very recently updated) and detailed instructions at http://bitbucket.org/galaxy/galaxy-central/wiki/cloud.
This seems extremely useful!
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This is a great platform having many useful tools available from the same place and interoperable. However, uploading big dataset to Galaxy is a challenge and a road block. I tried to upload a ILMN dataset of a few Gb and not yet done after a day and half. Any plan to enable Aspera-like tools to accelerate the data transfer speed?
Also, I think a blast tool that allows search against arbitrary database would be useful too. Any plan to add this feature?
Great job!
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Originally posted by tweist View PostThis is a great platform having many useful tools available from the same place and interoperable. However, uploading big dataset to Galaxy is a challenge and a road block. I tried to upload a ILMN dataset of a few Gb and not yet done after a day and half. Any plan to enable Aspera-like tools to accelerate the data transfer speed?
Also, I think a blast tool that allows search against arbitrary database would be useful too. Any plan to add this feature?
Great job!
- gzip them
- put them to a web-accessible loocation
- paste a URL pointing to your files to upload tool as shown in the attached image
Aspera is incredibly expensive to license, and we're not convinced it really accelerates things that much. There are some open source alternative we will be taking a look at
Yes, blasting against custom db is on the to do list as numerous people want this to happen.Attached Files
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Originally posted by nekrut View PostHi, upload limitations are going to be a problem for all of us as it is not Galaxy issue per se. To upload your files try this:
- gzip them
- put them to a web-accessible loocation
- paste a URL pointing to your files to upload tool as shown in the attached image
Aspera is incredibly expensive to license, and we're not convinced it really accelerates things that much. There are some open source alternative we will be taking a look at
Yes, blasting against custom db is on the to do list as numerous people want this to happen.
Ben
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I have uploaded a gzipped 300 MB .qual file and it works for doing box plot. perhaps your fren didn't complete the upload?
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Originally posted by ezilybored View PostHi there, sorry if i am being naive but will galaxy be able to read the files as gzips? a colleague of mine tried recently and said that it wasnt able to read the file format.
Ben
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I'm having a similar problem to Ben, I have illumina fastq files that are gzipped. I can upload them in a few minutes but then when I try to do the groomer i get this error:
An error occurred running this job: Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in <module>
if __name__ == "__main__": main()
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main
Is there some sort of facility to unzip gz files? Thanks, J
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Originally posted by ezilybored View PostHi there, sorry if i am being naive but will galaxy be able to read the files as gzips? a colleague of mine tried recently and said that it wasnt able to read the file format.
Ben
Originally posted by James View PostI'm having a similar problem to Ben, I have illumina fastq files that are gzipped. I can upload them in a few minutes but then when I try to do the groomer i get this error:
An error occurred running this job: Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in <module>
if __name__ == "__main__": main()
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main
Is there some sort of facility to unzip gz files? Thanks, J
Galaxy does not yet accept .tar(.gz) nor .zip files. Each file needs to be gzip'd individually (without tar'ing) in order for it it work with the upload tool at this time.
Support for .tar(.gz) and .zip files is being investigated.
Please don't hesitate to let us know if we can be of further help. Thanks for using Galaxy.
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