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Free & Open Environment for NGS analysis: Galaxy (http://usegalaxy.org)

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  • #16
    Originally posted by nilshomer View Post
    The indexes in the manual work very well and support most types of sequence data (lengths and technologies) and genomes (long and short). Given this information, it should be trivial to get BFAST support up and running. Feel free to PM me or email me.
    Great. We'll give it a shot and make a wrapper in a few weeks.

    Comment


    • #17
      New Quickies explaining fastq manipulation

      Just added two movies explaining fastq manipulation: basic and advanced.

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      • #18
        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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        • #19
          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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          • #20
            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!

            Comment


            • #21
              Originally posted by tweist View Post
              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!
              Hi, 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.
              Attached Files

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              • #22
                Hi,

                Have you looked at open source alternative such as UDT to address the data transfer bottleneck? Also, is there a limit on how much data that I can save in my galaxy account? Thanks!

                Comment


                • #23
                  Originally posted by tweist View Post
                  Hi,
                  Also, is there a limit on how much data that I can save in my galaxy account? Thanks!
                  No limit as of now

                  Comment


                  • #24
                    Originally posted by nekrut View Post
                    Hi, 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.
                    Hi 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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                    • #25
                      I have uploaded a gzipped 300 MB .qual file and it works for doing box plot. perhaps your fren didn't complete the upload?
                      http://kevin-gattaca.blogspot.com/

                      Comment


                      • #26
                        Originally posted by ezilybored View Post
                        Hi 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
                        Yes, you can. The best way to get data in is to upload gzipped files via URL (http and ftp both work). See post #21 in the thread (scroll up).

                        Comment


                        • #27
                          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

                          Comment


                          • #28
                            Originally posted by ezilybored View Post
                            Hi 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 Post
                            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
                            Galaxy does support the upload of gzip'd files.

                            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.

                            Comment


                            • #29
                              Is there any way that Galaxy can be used to analyze data from a Helicos machine?

                              Comment


                              • #30
                                Originally posted by Calico View Post
                                Is there any way that Galaxy can be used to analyze data from a Helicos machine?
                                We have not see the data ourselves yet, but I just asked Helicos guys to send us a few files. Do you have any to share?

                                Comment

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