Dear GalaxyTeam members, I'm a PhD student at the University of Canterbury and I have been using Galaxy for about 3 weeks... It is an excellent program! Actually it is the kind of tool I was looking for many months and an awesome complement for the UCSC Genome Browser Until now I have worked mostly using the interface at http://test.g2.bx.psu.edu/ which I guess is the test version. I have also installed the program in my linux session, however, I work more often in windows. Therefore I would like to know if you have a binary (or if you plan to make one) to run the program in windows? And a curiosity: where are the files from the history saved? What is the size limit for all the history files? Many thanks for your cool tool! Iris ====================================== Iris M. Vargas Jentzsch PhD Student School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 (7048) e-mail: imj15@student.canterbury.ac.nz
Iris, Thanks for your interest. Galaxy will run under Windows if you have Cygwin (http://www.cygwin.com/) installed. You will need make sure you have the latest version of Galaxy from SVN. Files are saved under "database/files/". There is no maximum file size in Galaxy, although certain filesystems do have limits (ie FAT32 has a max of 4GB). Let us know if you encounter a file size error. Don't hesitate to let us know if we can offer more help, Dan On Tue, 18 Jul 2006, Iris Vargas Jentzsch wrote:
Dear GalaxyTeam members,
I'm a PhD student at the University of Canterbury and I have been using Galaxy for about 3 weeks... It is an excellent program! Actually it is the kind of tool I was looking for many months and an awesome complement for the UCSC Genome Browser
Until now I have worked mostly using the interface at http://test.g2.bx.psu.edu/ which I guess is the test version. I have also installed the program in my linux session, however, I work more often in windows. Therefore I would like to know if you have a binary (or if you plan to make one) to run the program in windows?
And a curiosity: where are the files from the history saved? What is the size limit for all the history files?
Many thanks for your cool tool!
Iris
====================================== Iris M. Vargas Jentzsch PhD Student School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand
phone: +64 (0) 3 364 2987 (7048) e-mail: imj15@student.canterbury.ac.nz
Hello Galaxy-team members, I downloaded the last version of Galaxy yesterday and tried to install it and run it under Windows XP. After installing Cygwin and Galaxy and making sure that both are in my path, I could not get the program to run. It seems to be missing some files (that are actually there). The message printed to the screen is as follows: imj15@biolz215 /cygdrive/c/Galaxy $ ./run.sh Architecture appears to be cygwin_nt-5.1-i686 python path: /cygdrive/c/Galaxy/modules:/cygdrive/c/Galaxy/eggs:/cygdrive/c/Gala xy/arch/cygwin_nt-5.1-i686/lib/python Traceback (most recent call last): File "paster.py", line 7, in ? command.run() File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/command.p y", line 70, in run File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/command.p y", line 110, in invoke File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/command.p y", line 205, in run File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/serve.py" , line 182, in command File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/serve.py" , line 202, in loadapp File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 183, in loadapp File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 204, in loadobj File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 578, in create File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 90, in invoke File "/cygdrive/c/Galaxy/eggs/Paste-0.5.1dev_r4888-py2.4.egg/paste/urlmap.py", line 24, in urlmap_factory File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 263, in get_app File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 275, in app_context File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 369, in get_context File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 411, in _context_from_explicit File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi. py", line 14, in import_string File "/cygdrive/c/GAlaxy/modules/pkg_resources.py", line 1627, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/cygdrive/c/GAlaxy/universe_wsgi.py", line 4, in ? import galaxy.model.mapping File "/cygdrive/c/GAlaxy/galaxy/model/mapping.py", line 8, in ? pkg_resources.require( "pysqlite>=2", "sqlalchemy>=0.2" ) File "/cygdrive/c/GAlaxy/modules/pkg_resources.py", line 503, in require needed = self.resolve(parse_requirements(requirements)) File "/cygdrive/c/GAlaxy/modules/pkg_resources.py", line 482, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: pysqlite>=2 Could you please let me know what could be going wrong here? Another question: Is there a possibility to run Galaxy directly from the command line to automate some repetitive tasks? Thank you! Iris ====================================== Iris M. Vargas Jentzsch School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 ext 7048 ----- Original Message ----- From: "Dan Blankenberg" <djb396@bx.psu.edu> To: "Iris Vargas Jentzsch" <imj15@student.canterbury.ac.nz> Cc: <galaxy-user@bx.psu.edu> Sent: Tuesday, July 18, 2006 6:49 AM Subject: Re: [Galaxy-user] some questions
Iris,
Thanks for your interest. Galaxy will run under Windows if you have Cygwin (http://www.cygwin.com/) installed. You will need make sure you have the latest version of Galaxy from SVN.
Files are saved under "database/files/".
There is no maximum file size in Galaxy, although certain filesystems do have limits (ie FAT32 has a max of 4GB). Let us know if you encounter a file size error.
Don't hesitate to let us know if we can offer more help,
Dan
On Tue, 18 Jul 2006, Iris Vargas Jentzsch wrote:
Dear GalaxyTeam members,
I'm a PhD student at the University of Canterbury and I have been using Galaxy for about 3 weeks... It is an excellent program! Actually it is the kind of tool I was looking for many months and an awesome complement for the UCSC Genome Browser
Until now I have worked mostly using the interface at http://test.g2.bx.psu.edu/ which I guess is the test version. I have also installed the program in my linux session, however, I work more often in windows. Therefore I would like to know if you have a binary (or if you plan to make one) to run the program in windows?
And a curiosity: where are the files from the history saved? What is the size limit for all the history files?
Many thanks for your cool tool!
Iris
====================================== Iris M. Vargas Jentzsch PhD Student School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand
phone: +64 (0) 3 364 2987 (7048) e-mail: imj15@student.canterbury.ac.nz
Iris, First off, thanks for your detailed message. As it turns out, a new version of Cygwin (1.5.21) was released, which required a new set of eggs to be created. I have added these eggs to the repository. If you do an "svn up" these eggs should be downloaded for you. Please let me know if this does not resolve your problems. As far as automating tasks within Galaxy, there is not currently a way to do this - it is, however, something that we are interested it. As an alternative, Galaxy's tools are able to be executed directly from the command line (results will not appear in Galaxy), using input and output files. Please let me know if there is anything else that we can do to help, Dan On Thu, 24 Aug 2006, Iris Vargas Jentzsch wrote:
Hello Galaxy-team members,
I downloaded the last version of Galaxy yesterday and tried to install it and run it under Windows XP. After installing Cygwin and Galaxy and making sure that both are in my path, I could not get the program to run. It seems to be missing some files (that are actually there). The message printed to the screen is as follows:
imj15@biolz215 /cygdrive/c/Galaxy
$ ./run.sh
Architecture appears to be cygwin_nt-5.1-i686
python path: /cygdrive/c/Galaxy/modules:/cygdrive/c/Galaxy/eggs:/cygdrive/c/Gala
xy/arch/cygwin_nt-5.1-i686/lib/python
Traceback (most recent call last):
File "paster.py", line 7, in ?
command.run()
File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/command.p
y", line 70, in run
File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/command.p
y", line 110, in invoke
File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/command.p
y", line 205, in run
File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/serve.py"
, line 182, in command
File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/serve.py"
, line 202, in loadapp
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 183, in loadapp
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 204, in loadobj
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 578, in create
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 90, in invoke
File "/cygdrive/c/Galaxy/eggs/Paste-0.5.1dev_r4888-py2.4.egg/paste/urlmap.py",
line 24, in urlmap_factory
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 263, in get_app
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 275, in app_context
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 369, in get_context
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 411, in _context_from_explicit
File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadwsgi.
py", line 14, in import_string
File "/cygdrive/c/GAlaxy/modules/pkg_resources.py", line 1627, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/cygdrive/c/GAlaxy/universe_wsgi.py", line 4, in ?
import galaxy.model.mapping
File "/cygdrive/c/GAlaxy/galaxy/model/mapping.py", line 8, in ?
pkg_resources.require( "pysqlite>=2", "sqlalchemy>=0.2" )
File "/cygdrive/c/GAlaxy/modules/pkg_resources.py", line 503, in require
needed = self.resolve(parse_requirements(requirements))
File "/cygdrive/c/GAlaxy/modules/pkg_resources.py", line 482, in resolve
raise DistributionNotFound(req) # XXX put more info here
pkg_resources.DistributionNotFound: pysqlite>=2
Could you please let me know what could be going wrong here?
Another question: Is there a possibility to run Galaxy directly from the command line to automate some repetitive tasks?
Thank you!
Iris
====================================== Iris M. Vargas Jentzsch School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 ext 7048
----- Original Message ----- From: "Dan Blankenberg" <djb396@bx.psu.edu> To: "Iris Vargas Jentzsch" <imj15@student.canterbury.ac.nz> Cc: <galaxy-user@bx.psu.edu> Sent: Tuesday, July 18, 2006 6:49 AM Subject: Re: [Galaxy-user] some questions
Iris,
Thanks for your interest. Galaxy will run under Windows if you have Cygwin (http://www.cygwin.com/) installed. You will need make sure you have the latest version of Galaxy from SVN.
Files are saved under "database/files/".
There is no maximum file size in Galaxy, although certain filesystems do have limits (ie FAT32 has a max of 4GB). Let us know if you encounter a file size error.
Don't hesitate to let us know if we can offer more help,
Dan
On Tue, 18 Jul 2006, Iris Vargas Jentzsch wrote:
Dear GalaxyTeam members,
I'm a PhD student at the University of Canterbury and I have been using Galaxy for about 3 weeks... It is an excellent program! Actually it is the kind of tool I was looking for many months and an awesome complement for the UCSC Genome Browser
Until now I have worked mostly using the interface at http://test.g2.bx.psu.edu/ which I guess is the test version. I have also installed the program in my linux session, however, I work more often in windows. Therefore I would like to know if you have a binary (or if you plan to make one) to run the program in windows?
And a curiosity: where are the files from the history saved? What is the size limit for all the history files?
Many thanks for your cool tool!
Iris
====================================== Iris M. Vargas Jentzsch PhD Student School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand
phone: +64 (0) 3 364 2987 (7048) e-mail: imj15@student.canterbury.ac.nz
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participants (2)
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Dan Blankenberg -
Iris Vargas Jentzsch