Anyone install galaxy local mirror successfully under Windows?
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! -- Daofeng Li,PhD Candidate China Agricultural University
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 galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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@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@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
-- Daofeng Li,PhD Candidate China Agricultural University
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@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@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
------------------------------------------------------------------------
------------------------------------------------------------------------
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@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@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@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
------------------------------------------------------------------------
------------------------------------------------------------------------
-- Daofeng Li,PhD Candidate China Agricultural University
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@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@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@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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@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@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@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@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
------------------------------------------------------------------------
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
-- Daofeng Li,PhD Candidate China Agricultural University
participants (3)
-
Daofeng Li -
Nate Coraor -
Sebastian J. Schultheiss