Question: Problems Installing Galaxy Under Cygwin
gravatar for Iris Vargas Jentzsch
12.3 years ago by
Iris Vargas Jentzsch50 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 $ ./ 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 "", line 7, in ? File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/comman d.p y", line 70, in run File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/comman d.p y", line 110, in invoke File "/cygdrive/c/Galaxy/eggs/PasteScript-0.5-py2.4.egg/paste/script/comman d.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/loadws gi. py", line 183, in loadapp File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 204, in loadobj File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 578, in create File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 90, in invoke File "/cygdrive/c/Galaxy/eggs/Paste-0.5.1dev_r4888-py2.4.egg/paste/urlmap.p y", line 24, in urlmap_factory File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 263, in get_app File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 275, in app_context File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 369, in get_context File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 411, in _context_from_explicit File "/cygdrive/c/Galaxy/eggs/PasteDeploy-0.5-py2.4.egg/paste/deploy/loadws gi. py", line 14, in import_string File "/cygdrive/c/GAlaxy/modules/", line 1627, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/cygdrive/c/GAlaxy/", line 4, in ? import galaxy.model.mapping File "/cygdrive/c/GAlaxy/galaxy/model/", line 8, in ? pkg_resources.require( "pysqlite>=2", "sqlalchemy>=0.2" ) File "/cygdrive/c/GAlaxy/modules/", line 503, in require needed = self.resolve(parse_requirements(requirements)) File "/cygdrive/c/GAlaxy/modules/", 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 To: "Iris Vargas Jentzsch" <> Cc: <> Subject: Re: [Galaxy-user] some questions
galaxy • 1.1k views
ADD COMMENTlink modified 12.3 years ago by Dan Blankenberg130 • written 12.3 years ago by Iris Vargas Jentzsch50
gravatar for Dan Blankenberg
12.3 years ago by
Dan Blankenberg130 wrote:
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
ADD COMMENTlink written 12.3 years ago by Dan Blankenberg130
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