Hi Dannon,

I pulled the new updates and restarted galaxy. However, the issue is not resolved. Is there other information you might need?

hg summary:

parent: 9332:0f51ae4f1c84 tip
 Unicode fixes for workflow names in Tool Menu.
branch: stable

Best,

Geert


On 05/21/2013 06:08 PM, Dannon Baker wrote:
Ok, so you're running the old tip of -dist. There are a few new updates you can retrieve using `hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central` <http://bitbucket.org/galaxy/galaxy-central%60>.

-Dannon


On Tue, May 21, 2013 at 12:01 PM, Geert Vandeweyer <geert.vandewey...@ua.ac.be <mailto:geert.vandewey...@ua.ac.be>> wrote:

    hg summary:

    parent: 9320:47ddf167c9f1 tip
     Use Galaxy's ErrorMiddleware since Paste's doesn't return
    start_response.  Fixes downloading tarballs from the Tool Shed
    when use_debug = false.
    branch: stable
    commit: 18 modified, 178 unknown
    update: (current)


    Geert


    On 05/21/2013 04:59 PM, Dannon Baker wrote:
    Geert,

    This should be fixed in the up-to-date stable branch as far as I
    know.  Can you tell me what 'hg summary' states?

    -Dannon


    On Mon, May 20, 2013 at 4:43 PM, Geert Vandeweyer
    <geert.vandewey...@ua.ac.be <mailto:geert.vandewey...@ua.ac.be>>
    wrote:

        Hi,

        After the latest upgrade (april), I'm having issues when
        starting (batch) workfows. Sometimes, it seems that step
        dependencies are not stored correctly, leading to some steps
        being started too soon, without prior datasets being
        completed. Specifically, for some workflows, some of the
        later steps start immediately. The issue seems to be random:
        in batch workflow submission, some run flawlessly, others
        show the issue, at different steps. I use one handler in the
        job_conf to exclude race conditions and shared variable clashes.

        I suspect there is an issue with fetching or storing the
        steps to/from the database (a remote mysql database in my
        case). On the mysql-side there are no errors in the log
        files, and the galaxy-logs don't show clear issues either.

        Does the job new job handler check for failed database
        connections? If not, could somebody point me to the code that
        performs these steps, I'd like to add a check & retry routine
        to see if this improves the situation.

        best,

        Geert

--
        Geert Vandeweyer, Ph.D.
        Department of Medical Genetics
        University of Antwerp
        Prins Boudewijnlaan 43
        2650 Edegem
        Belgium
        Tel: +32 (0)3 275 97 56
        E-mail: geert.vandewe...@ua.ac.be
        <mailto:geert.vandewe...@ua.ac.be>
        http://ua.ac.be/cognitivegenetics
        http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

        ___________________________________________________________
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--
    Geert Vandeweyer, Ph.D.
    Department of Medical Genetics
    University of Antwerp
    Prins Boudewijnlaan 43
    2650 Edegem
    Belgium
    Tel: +32 (0)3 275 97 56
    E-mail:geert.vandewe...@ua.ac.be  <mailto:geert.vandewe...@ua.ac.be>
    http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726



--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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