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!
On Fri, Mar 14, 2008 at 10:22 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
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
> <sebi(a)tuebingen.mpg.de> wrote:
>> 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
>>> <sebi(a)tuebingen.mpg.de> wrote:
>>>> 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!
>>>>>
>>>>>
>>>>>
>>>>>
------------------------------------------------------------------------
>>>>>
>>>>>
>>>>>
------------------------------------------------------------------------
>>>>>
>>>>>
>>>>>
------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> galaxy-user mailing list
>>>>> galaxy-user(a)bx.psu.edu
>>>>>
http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>>>
>>>
>>>
>>>
------------------------------------------------------------------------
>>>
>>>
>>>
------------------------------------------------------------------------
>>>
>>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user(a)bx.psu.edu
>
http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
--
Daofeng Li,PhD Candidate
China Agricultural University