Hi Song,

We have alpha support for Tophat v1.3.0 and it appears to work fine with Galaxy's Tophat wrappers. We'll upgrade and start full testing near term.


For now, when running in a local instances, we do encourage users to try it and see if it meets their needs. Perhaps try with an uncompressed version of the same input file and see if that functions as expected or if the same error is given when used with the Galaxy wrappers?

If you want to post testing details (Galaxy pull # from bitbucket, gzip, OS version and anything else you feel is relevant) after this sort of testing, the development team will use that information when full integration testing is performed.

Perhaps others running local instances will also comment if you post these detailed testing results to the galaxy-...@bx.psu.edu mailing list (will reach the primary external Galaxy development community).

Thanks for using Galaxy!

Jen
Galaxy team

On 7/20/11 6:59 AM, Song Li wrote:

Hi Jen,

Thank you for the fast reply, however, tophat works fine with this
command when used as stand alone software. I checked the version of gzip
and it's the same on galaxy server and on the machine where I run tophat
alone.

The broken pipe error is likely due to a file that is not closed by a
previous step.

Have anyone tested tophat 1.3 on galaxy?

Thanks,
Song

On Tue 07/19/11 6:45 PM , Jennifer Jackson <j...@bx.psu.edu> wrote:

    Hello Song Li,

    The file extension seems to be a mismatch.

    file.gz <- "gzip" utility

    Exploring the use of gunzip or zcat are options to restore a "file.z".

    Hopefully this helps,

    Jen
    Galaxy team

    On 7/19/11 11:52 AM, Song Li wrote:
    >  Hello everyone,
    >
    >  I was trying to run tophat in a local version of galaxy, but I got the
    >  following error:
    >
    >  gzip: stdout: Broken pipe
    >  [Tue Jul 19 14:10:36 2011] Processing bowtie hits
    >  Error: could not open pipe gzip -cd<
    ./tophat_out/tmp/left_kept_reads_missing.fq.z
    >
    >  It seems that when tophat is calling gzip, the pipe can not be open.
    >
    >  Can anyone suggest a fix to this problem?
    >
    >  Thanks,
    >  Song Li
    >  --
    >  Postdoctoral Associate
    >  Uwe Ohler Laboratory
    >  Institute for Genome Sciences and Policy
    >  101 Science Drive
    >  CIEMAS 2171
    >  Phone: 919-68-2124
    >  Duke University
    >
    >
    >
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    ___________________________________________________________
    The Galaxy User list should be used for the discussion of
    Galaxy analysis and other features on the public server
    at usegalaxy.org. Please keep all replies on the list by
    using "reply all" in your mail client. For discussion of
    local Galaxy instances and the Galaxy source code, please
    use the Galaxy Development list:

    http://lists.bx.psu.edu/listinfo/galaxy-dev <parse.php?redirect=<a
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--
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http://usegalaxy.org/
http://galaxyproject.org/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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