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  1. Deep Backlog
  2. DB-14

Examine IGB's ability to automate screenshots using scripts

          Details

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

            This power user wrote scripts to automate screen shots from another genome browser:

            https://twitter.com/chrisamiller/status/605116222586261504

            What’s stopping him (or anyone?) from doing this with IGB?

            To follow up, we need to test whether the IGB scripting language enables us to make screen captures of similar or better quality.

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                mason Mason Meyer (Inactive) added a comment -

                From Ivory:

                The first challenge that comes to mind for me is that IGB needs to be open in order for scripts to run. I can’t use IGB on our cluster, so I can’t run a script that makes images on our cluster.
                [another genome browser] seems to have a similar limitation which this guy addressed
                "This is complicated, because [another genome browser] demands that it actually pump the data to a display server, whether or not anyone is actually looking at it. The '[another genome browser]CreateSnapshots' script launches a non-displayed display server using Xvfb, sets the appropriate env variables, then runs [another genome browser] in batch mode.”
                I am not familiar with Xvfb, can that work for IGB as well?
                Even if it did, I think the scripts run from R take dimension parameters from the current IGB window…not sure how one would adjust those without the GUI interface.

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                mason Mason Meyer (Inactive) added a comment - From Ivory: The first challenge that comes to mind for me is that IGB needs to be open in order for scripts to run. I can’t use IGB on our cluster, so I can’t run a script that makes images on our cluster. [another genome browser] seems to have a similar limitation which this guy addressed "This is complicated, because [another genome browser] demands that it actually pump the data to a display server, whether or not anyone is actually looking at it. The ' [another genome browser] CreateSnapshots' script launches a non-displayed display server using Xvfb, sets the appropriate env variables, then runs [another genome browser] in batch mode.” I am not familiar with Xvfb, can that work for IGB as well? Even if it did, I think the scripts run from R take dimension parameters from the current IGB window…not sure how one would adjust those without the GUI interface.

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                  • Assignee:
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                    Reporter:
                    mason Mason Meyer (Inactive)
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                    • Created:
                      Updated: