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  1. Bug Repository
  2. BUG-421

Test Galaxy

          Details

          • Type: Task
          • Status: Reopened (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Labels:
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            Description

            go to the galaxy home site and upload (from URL) one bed, one bam, one wig, one bigbed and one bigwig. Load them up and open an instance of IGB. Use "local" (look in the right side history at the bottom of each file box) to visualize each type and be sure that they work... you should get a pop up telling you that you need to hit 'load' to see the data. don't uncheck it and make sure it keeps reappearing. Then try again with it unchecked. There may be several popups during the bam visualization. If you need more details, come ask me...

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                relates to

                Task - A task that needs to be done. BUG-647 Server bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

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                  ann.loraine Ann Loraine added a comment -

                  notes from Dan:

                  • docker containers for testing, a bit complex to
                  • manual local tests are a bit harder; they might not run
                  • you have to add the test for a new feature

                  Look at github for the tests and run testing code.

                  Show
                  ann.loraine Ann Loraine added a comment - notes from Dan: docker containers for testing, a bit complex to manual local tests are a bit harder; they might not run you have to add the test for a new feature Look at github for the tests and run testing code.
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                  ann.loraine Ann Loraine added a comment -

                  Please review for new information and add to our Galaxy testing story if you see fit. Then please re-close.

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                  ann.loraine Ann Loraine added a comment - Please review for new information and add to our Galaxy testing story if you see fit. Then please re-close.
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                  kkubiak Katharine Kubiak (Inactive) added a comment - - edited

                  Passed Windows v11716

                  Works fine when uploading to Galaxy from a desktop file (I loaded one bed, one bam, one wig, one bigbed and one bigwig and used the "local" button to visualize each in IGB).

                  When uploading to Galaxy from a URL I get an error within Galaxy because there is a username and password for the quickload. For example I pasted this link:

                  http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/cyto_processed/BA3.bed

                  into the "URL/Text:" box for uploading a file and I get this error:

                  "An error occurred running this job: Enter username for By invitation only at www.igbquickload.org: Unable to fetch http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/cyto_processed/BA3.bed
                  EOF when reading a line"

                  There is no where to put in a username and password.

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - - edited Passed Windows v11716 Works fine when uploading to Galaxy from a desktop file (I loaded one bed, one bam, one wig, one bigbed and one bigwig and used the "local" button to visualize each in IGB). When uploading to Galaxy from a URL I get an error within Galaxy because there is a username and password for the quickload. For example I pasted this link: http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/cyto_processed/BA3.bed into the "URL/Text:" box for uploading a file and I get this error: "An error occurred running this job: Enter username for By invitation only at www.igbquickload.org: Unable to fetch http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/ngs/cyto_processed/BA3.bed EOF when reading a line" There is no where to put in a username and password.

                    People

                    • Assignee:
                      pbadzuh Philip Badzuh (Inactive)
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      • Created:
                        Updated: