Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Add large bam files to Galaxy

    Hi guys,
    I installed a Galaxy instance on my computer (it is a Mac Pro, 12 GB Ram, 2.6 GHz quad core intel Xeon). I start the server on the terminal, and them I type on my browse the address 127.0.0.1:8080, and then the Galaxy is open in my browser. I think this is OK until this point.
    The problem comes when I try to add BAM files (~40GB) to Galaxy selecting "get data" and then "upload a file".
    I select my file, select the file type, and execute.
    During execution, the process seems to be very slow (really revy slow).
    Since the galaxy is running here on my computer, and the data is already on my hard disk, I think is something wrong, am I right?
    Is there a way to copy the BAM files to a specific folder into galaxy directory?
    Thank you guys!

  • #2
    See this page for instructions on adding files to galaxy from local file paths: http://wiki.galaxyproject.org/Admin/...ibrary%20Files

    Comment


    • #3
      Yup. The only way to add large files is as an admin. Get admin privileges (easy to do) then you can manage your data libraries very quickly and easy

      Comment


      • #4
        Admin privileges

        I was looking for information about how to get admin privileges, and didn't found a solution yet. I'll keep looking. If I do not find, I come back here to ask for help. Thank you a lot.
        (I am new on galaxy, still learning how it works)

        Comment


        • #5
          Originally posted by bfantinatti View Post
          I was looking for information about how to get admin privileges, and didn't found a solution yet. I'll keep looking. If I do not find, I come back here to ask for help. Thank you a lot.
          (I am new on galaxy, still learning how it works)

          Comment


          • #6
            "Setup admin user

            To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini.

            # this should be a comma-separated list of valid Galaxy users
            admin_users = [email protected],[email protected]

            When an admin user logs into Galaxy, they will see an "Admin" menu item on the top Galaxy menu bar which will take them to the Galaxy Admin page."

            Comment


            • #7
              Problem

              Hey guys, I have already added my user e-mail on that list as both you said, reloaded the server (sh run.sh --reload) and then 127.0.0.1:8080 on by browser. Nothing different happened. I couldn't find the Administration Menu.
              Trying to login with the e-mail, galaxy says: No such user... Did I do something wrong?

              The e-mail I added to the list is the same I used to cadastre in Galaxy site.

              Comment


              • #8
                Hi,
                I have a very similar problem (uploading fastq on my local GALAXY server taking extremely slow).
                Was your problem solved, bfantinatti?? If so, how??

                Comment


                • #9
                  It was slow because you are UPLOADING your local file to your local Web Server by HTTP protocol and then the Web server will save this file again to a new place, so the rest of the system can See it, a very nonsense operation, thus they suggest you to be admin then you can just tell the system where the local file is. Hope this helps.

                  Comment


                  • #10
                    No

                    I still did not solve the problem, Hiroki.
                    My problem is in this moment to create a admin account. I have already added my e-mail to the configuration file and nothing happens. I still can not log as admin.
                    Is there another operation to get admin access?
                    Thank you

                    Comment


                    • #11
                      When you create the local instance you can use it right away as anonymous user, without login, unless you disable this option in universe_wsgi.ini. To get administrative privileges as a user, you have to create that user, that is simply register yourself with the credentials you put in the configuration file. That worked for me.

                      Comment


                      • #12
                        Also, galaxy gurus recommend to replace the default minimal database engine with a real database, like PostgreSQL or MySQL if dealing with large datasets. It is quite a hassle though, at least it was for me, as numerous instructions not always worked on my machine, but it eliminated hangups and interrupted transfers.

                        Comment


                        • #13
                          Hi guys,

                          Thanks. So I understand I must to be admin user to handle large files on Galaxy.
                          But like bfantinatti, I still don't know how to be admin user....

                          Comment


                          • #14
                            As bfantinatti did, I edited universe_wsgi.ini by adding my email address and of course removed # from the line.
                            I reload run.sh and tried to log in with my email address. But it says "no such user".
                            Also how can I set the password??

                            Comment


                            • #15
                              Originally posted by Hiroki View Post
                              Hi guys,

                              Thanks. So I understand I must to be admin user to handle large files on Galaxy.
                              But like bfantinatti, I still don't know how to be admin user....
                              No you do not have to be admin to handle large files, but you have to be to enable other upload options. As admin you can give permission to other users to upload files using FTP or from local directories. You also have to be admin to create libraries, add and manipulate datasets in libraries, etc, unless you give certain permissions to users.

                              On the left side of the menu bar in drop-down menu 'User' you can register as user and create password. If you do not see option 'Register', look in 'Security' section of universe_wsgi, there are several options concerning users. Obviously, you need to restart galaxy after modification of this config file. Let me know if the issue was not resolved.

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Current Approaches to Protein Sequencing
                                by seqadmin


                                Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                                04-04-2024, 04:25 PM
                              • seqadmin
                                Strategies for Sequencing Challenging Samples
                                by seqadmin


                                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                03-22-2024, 06:39 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, 04-11-2024, 12:08 PM
                              0 responses
                              18 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 04-10-2024, 10:19 PM
                              0 responses
                              22 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 04-10-2024, 09:21 AM
                              0 responses
                              16 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 04-04-2024, 09:00 AM
                              0 responses
                              47 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X