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  1. IGB
  2. IGBF-2430

Check quickload instructions

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Blocker
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:

          Description

          Recently a researcher asked about these quickload instructions from the User's Guide:

          He wrote:

          Is this method still the easiest way to upload BAM/BED files to IGB Quickload?

          The last edit to this page was in Jan 2016. The content may be out of date.

          Before we answer the question, we should check that the content is still correct.

          To do this, try to follow the instructions to set up a satellite Quickload site on your computer, using the latest tomato genome currently available in IGB. Make note of any problems you encounter. Your test QL site should include a BED and a BAM file, since this is what the researcher asked about. You can get examples from the RNA-Seq quickload site.

          Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions.

          If you run into problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Include it in the current sprint.

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              relates to

              Task - A task that needs to be done. IGBF-2454 Edit quickload instructions wiki for clarity

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

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                4 older comments
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                rweidenh Logan Weidenhammer (Inactive) added a comment -

                IGBF-2454 created.

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                rweidenh Logan Weidenhammer (Inactive) added a comment - IGBF-2454 created.
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                ann.loraine Ann Loraine added a comment -

                Thanks for the detailed notes Logan Weidenhammer and Nowlan Freese !

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                ann.loraine Ann Loraine added a comment - Thanks for the detailed notes Logan Weidenhammer and Nowlan Freese !
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                rweidenh Logan Weidenhammer (Inactive) added a comment -

                [~aloraine] Do we want to investigate the http://www.igbquickload.org/quickload/ large-file download problem?

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                rweidenh Logan Weidenhammer (Inactive) added a comment - [~aloraine] Do we want to investigate the http://www.igbquickload.org/quickload/ large-file download problem?
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                nfreese Nowlan Freese added a comment -

                The issue I ran into was on the scidas server: http://lorainelab-quickload.scidas.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/

                The scidas data load in IGB and I can curl the data on my laptop, but clicking on the file and trying to download through the browser appears to be blocked.

                Show
                nfreese Nowlan Freese added a comment - The issue I ran into was on the scidas server: http://lorainelab-quickload.scidas.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/ The scidas data load in IGB and I can curl the data on my laptop, but clicking on the file and trying to download through the browser appears to be blocked.
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                ann.loraine Ann Loraine added a comment -

                I am OK with this as it could protect people from accidentally try to download a multi-Gb sized file.

                Moving to closed.

                Show
                ann.loraine Ann Loraine added a comment - I am OK with this as it could protect people from accidentally try to download a multi-Gb sized file. Moving to closed.

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: