Question: Problems Installing Galaxy Under Cygwin
0
Iris Vargas Jentzsch • 50 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/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/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
To: "Iris Vargas Jentzsch" <imj15@student.canterbury.ac.nz>
Cc: <galaxy-user@bx.psu.edu>
Subject: Re: [Galaxy-user] some questions
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modified 12.3 years ago
by
Dan Blankenberg • 130
•
written
12.3 years ago by
Iris Vargas Jentzsch • 50
