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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1113 ] Invoking biolegato fails on systems without zenity
    Date:
    02/19/11 13:26
    Submitted by:
    umhameld
    Assigned to:
    B_Fristensky
    Category:
    bioLegato
    Priority:
    3
    Ticket group:
    bioLegato
    Resolution:
    Not Resolved
    Summary:
    Invoking biolegato fails on systems without zenity
    Original submission:
    Observed behavior:

    Invoking "biolegato" from the command line fails saying at line 3 in biolegato "zenity not found" on systems without zenity installed.

    Expected behavior:

    Biolegato should not need zenity as a dependency, unless we add this to the list of dependencies for BIRCH, or include it ourselves.

    Steps to reproduce:

    Install BIRCH on a system without zenity, attempt to invoke biolegato through wrapper.


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    Followups
    Comment Date By
    This script works fine on systems without zenity, closing this bug. 03/12/11 11:28 umhameld
    I have modified /home/psgendb/script/biolegato to as described in the previous posting. Now it checks for zenity, and if it doesn't find it, just cat's the message to the terminal. Dale, please try this on your zenity-minus system.

    (Isn't this a good illustration of why a repo makes sense for distributing new copies of a script? We'll get there.)
    02/19/11 18:52 B_Fristensky
    Gads! You can't depend on anything in this life. This should only affect cases where someone types 'biolegato' at the command line. This was intended as a backward compatability measure to phase out 'biolegato' in favor of 'bldna', 'blprotein' etc.

    1. Dale, please check on your zenity-minus system whether 'bldna', 'blprotein', 'birch', 'blmarker' and 'bltree' correctly launch those interfaces.

    2. The old $BIRCH/script/biolegato script has been replaced in the current Devel. version with a script that does nothing but print a message saying to use one of those 5 commands. This is so users of BIRCH 2.7 or earlier aren't totally lost as to how to launch biolegato. The fix is probably to modify the script to look for zenity. If it's there then we use zenity to print to message from $BIRCH/script/biolegato.msg. Otherwise, we just cat the message to the terminal window. I will take care of this one
    02/19/11 18:06 B_Fristensky
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    Ticket change history
    Field Old value Date By
    status_id Open 03/12/11 11:28 umhameld
    close_date 12/31/69 19:00 03/12/11 11:28 umhameld
    priority 5 02/21/11 17:07 B_Fristensky
    resolution_id Unset 02/19/11 18:52 B_Fristensky
    status_id Pending 02/19/11 18:06 B_Fristensky
    assigned_to unset 02/19/11 18:06 B_Fristensky

     

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