Hi nate,
i checked the directory "E:\cygwin\galaxy_dist\tools\data_source"
there are actually many encode_* files
cannot i change some config to make it work? (and i dont know to change what,^_^)
so wo hpoe this limitation will be solved as soon as possible
Thanks for your reply and your team's galaxy:)
ps,i think the "galaxy in windows" page need to add require Cheetah version 1.0
Best Regards!
> Hi Daofeng,
>
> The location of ENCODE datasets is hard-coded in to the tools' configs
> (in tools/data_source/encode_*). Currently, external local data used by
> Galaxy is not handled via a standardized method. This is a limitation
> that we're working on removing.
>
> --nate
>
>
> Daofeng Li wrote:
> > Hi,
> >
> > Thanks:)
> > i attached the two files with this mail
> > yes, i am using cygwin
> > all i input is in cygwin, include python 2.4 installed in the cygwin
> > not in windows
> > but i also have galaxy installed on a CentOS server
> > same error still occur
> > i agree with you maybe need to download the encode data and put it in
> > the right directory
> > i checked the svn directory in the Galaxy offical site, with no found
> > whatever, that's fine
> > only this function can not use
> > and in the latest galaxy version have no EMBOSS utils
> > Thanks for your time and reply.
> >
> > Best Regards!
> >
> >
> > On Fri, Mar 14, 2008 at 6:06 PM, Sebastian J. Schultheiss
> >> Hello,
> >>
> >> the output you are seeing in your command prompt window is only a small
> >> part of what galaxy will show you during startup. Maybe you can try to
> >> redirect the output by calling the run.sh like this:
> >> sh run.sh > stdout.txt 2> stderr.txt
> >> which will create these two files and you can send them along for error
> >> finding.
> >>
> >> Didn't you say you were using cygwin? That should have its own console
> >> which can save much more output in its buffer, maybe you can try running
> >> galaxy in there.
> >>
> >> In the startup messages you will be able to see if a tool really
> >> produces an error or if it's just a dataset missing. In the case you
> >> sent today, it's actually only the missing data that is causing the error.
> >>
> >> The error message is the part where it says in a large font "No such
> >> file or directory: '/depot/data2/galaxy/encode_datasets.1'"
> >>
> >> As you can see from the path, this is not a windows-style path with
> >> drive letters and backslashes. To get rid of this message and use the
> >> encode datasets, you need to to the following:
> >>
> >> * download the encode datasets to your computer (sorry, I don't know how
> >> to get those)
> >> * change the path in the encode tool from
> >> /depot/data2/galaxy/encode_datasets.* to somewhere on your computer (can
> >> also be relative, e.g. '..\\galaxy_data\\encode\\' or something like that.
> >>
> >> Many of the other tools also have 'external' requirements, e.g. all the
> >> EMBOSS tools are just wrappers for the corresponding binaries, which
> >> need to be present in your path in order to use the tools in galaxy.
> >>
> >> Hope to help,
> >>
> >>
> >> -- Sebastian
> >>
> >>
> >> Daofeng Li wrote:
> >>> Hi Sebastian,
> >>>
> >>> Thank you for your response.
> >>> i remove Cheetah 2.0.1 and download Cheetah 1.0 from
sf.net > >>> use easy_install install it
> >>> now most problem soloved
> >>> most function can use normally now
> >>> but the tools under GET ENCODE DATA still have some errors
> >>> i wonder maybe some installed eggs wrong version
> >>> but i have no idea which egg is
> >>> do you have any experience with this problem
> >>> i attached the pic with this mail
> >>> Thanks for your time.
> >>>
> >>> Best Regards!
> >>>
> >>> On Thu, Mar 13, 2008 at 10:49 PM, Sebastian J. Schultheiss
> >>>> Hi there,
> >>>>
> >>>> from the error message you supplied, I think it has to do with the
> >>>> Cheetah module in python. Can you check whether the Cheetah you have
> >>>> installed is version 1.0? Galaxy only works with 1.0 and will give
> >>>> exactly this error message when it finds version 2.0 instead.
> >>>>
> >>>> I've had the same problem with an Ubuntu Linux system and we solved it
> >>>> by uninstalling Cheetah and using the supplied 1.0 egg. Maybe you can do
> >>>> the same under Winows.
> >>>>
> >>>> I'm not sure if Galaxy is supported under cygwin, so maybe you will
> >>>> encounter further problems...
> >>>>
> >>>> -- Sebastian
> >>>>
> >>>>
> >>>>
> >>>> Daofeng Li wrote:
> >>>>> Hi, Dear list members,
> >>>>>
> >>>>> i am trying to make a local mirror of galaxy under windows
> >>>>> it seems be very difficult
> >>>>> i succeded under a linux machine
> >>>>> the same step can not work on my Windows machine
> >>>>> is that means i need to build the specific egg for windows?
> >>>>> i am using cygwin and install python 2.4.4 in cygwin system,not
> >>>>> activepython in Win system
> >>>>> and use easy_install ti intsall any needed eggs under cygwin
> >>>>> i can also run the run.sh
> >>>>> but when i visit the page
> >>>>> there are so many errors...
> >>>>> error page and log page i had captured and attached with this mail
> >>>>>
> >>>>> can anyone give some suggestions?
> >>>>>
> >>>>> Best Regards!
> >>>>>
> >>>>>
> >>>>>
> >>>>> ------------------------------------------------------------------------
> >>>>>
> >>>>>
> >>>>> ------------------------------------------------------------------------
> >>>>>
> >>>>>
> >>>>> ------------------------------------------------------------------------
> >>>>>
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> >>>>> galaxy-user mailing list
> >>>
> >>>
> >>>
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> >>>
> >>>
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> >>>
> >>
> >
> >
> >
> >
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> >
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>
>
--
Daofeng Li,PhD Candidate
China Agricultural University