Question: [Bug] Errors With Cheetah On Intel Mac?
0
Jacob Biesinger • 40 wrote:
Hi.
I just checked out the latest version of galaxy and went through
installation. I'm writing to note the issues I've encountered thus
far.
A number of eggs were missing for my platform (Intel Mac OS 10.4,
python
2.5) and I had to scramble a number of eggs. These included the
following:
pycrypto
lzo_python
Cheetah
pysqlite
bx_python
Scrambling my own eggs worked fine except for with pysqlite. I grabbed
version 3.5.4 of sqlite3.c file and built a static pysqlite egg file.
When I first ran run.sh, the web server loaded just fine. But on
attempting
to upload a file, I got the following dump, which says to me that
galaxy is
using a local install of Cheetah rather than the egg that I scrambled:
URL: http://localhost:8080/tool_runner?tool_id=upload1
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/WebError-0.8a-
py2.5.egg/weberror/evalexception/middleware.py',
line 364 in respond
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.eg
g/paste/debug/prints.py',
line 98 in __call__
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.eg
g/paste/wsgilib.py',
line 539 in intercept_output
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Beaker-0.5-py2.5.egg
/beaker/session.py',
line 103 in __call__
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.eg
g/paste/recursive.py',
line 80 in __call__
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.eg
g/paste/httpexceptions.py',
line 632 in __call__
File '/Users/wjb/Projects/galaxy/lib/galaxy/web/framework/base.py',
line 123
in __call__
body = method( trans, **kwargs )
File '/Users/wjb/Projects/galaxy/lib/galaxy/web/controllers/tool_runne
r.py',
line 42 in index
return trans.fill_template( template, history=history,
toolbox=toolbox,
tool=tool, util=util, **vars )
File
'/Users/wjb/Projects/galaxy/lib/galaxy/web/framework/__init__.py',
line
356 in fill_template
searchList=[kwargs, self.template_context, dict(caller=self, t=self,
h=webhelpers, util=util, request=self.request, response=self.response,
app=self.app)] )
File
'/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.
3-i386.egg/Cheetah/Template.py',
line 1192 in __init__
self._compile(source, file, compilerSettings=compilerSettings)
File
'/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.
3-i386.egg/Cheetah/Template.py',
line 1480 in _compile
keepRefToGeneratedCode=True)
File
'/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.
3-i386.egg/Cheetah/Template.py',
line 777 in compile
raise e
IndentationError: expected an indented block
_Users_wjb_Projects_galaxy_templates_tool_form_tmpl.py, line 226)
I removed my /opt/local installation of Cheetah (and a few other
dependencies in /opt/local that I thought might affect building). I
then
started again on installation by removing the eggs directory and
running
setup.sh again. The above listed dependencies were not found again. I
scrambled them (including pysqlite as static) and tried to run run.sh
once
again. Now I am getting the following error:
Using eggs in py2.5-noplatform
Using eggs in py2.5-macosx-10.3-i386-ucs2
Checking Galaxy eggs
All eggs are up to date for this revision of Galaxy
python path:
/Users/wjb/Projects/galaxy/lib:/Users/wjb/Projects/galaxy/eggs/py2.5-n
oplatform:/Users/wjb/Projects/galaxy/eggs/py2.5-macosx-10.3-i386-ucs2
path:
/opt/local/bin:/opt/local/sbin:/usr/local/bin:/bin:/sbin:/usr/bin:/usr
/sbin:/usr/local/bin:/usr/texbin:/Library/Frameworks/Python.framework/
Versions/Current/bin:/usr/local/mysql/bin:/opt/local/lib/postgresql82/
bin:/depot/apps/i386/bin:/home/universe/darwin-i386/EMBOSS-5.0.0/bin:/
home/universe/darwin-i386/ImageMagick/bin:/home/universe/darwin-i386/P
AML/paml3.15/bin
Traceback (most recent call last):
File "./scripts/paster.py", line 11, in <module>
command.run()
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py
2.5.egg/paste/script/command.py",
line 78, in run
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py
2.5.egg/paste/script/command.py",
line 117, in invoke
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py
2.5.egg/paste/script/command.py",
line 212, in run
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py
2.5.egg/paste/script/serve.py",
line 227, in command
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py
2.5.egg/paste/script/serve.py",
line 250, in loadapp
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 193, in loadapp
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 213, in loadobj
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 237, in loadcontext
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 267, in _loadconfig
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 397, in get_context
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 439, in _context_from_explicit
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py
2.5.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
File "/Users/wjb/Projects/galaxy/lib/pkg_resources.py", line 1912,
in load
try:
File "/Users/wjb/Projects/galaxy/lib/galaxy/web/__init__.py", line
5, in
<module>
from framework import expose, json, url_for, error, FormBuilder
File
"/Users/wjb/Projects/galaxy/lib/galaxy/web/framework/__init__.py",
line 9, in <module>
from Cheetah.Template import Template
File "build/bdist.macosx-10.3-i386/egg/Cheetah/Template.py", line
47, in
<module>
File "build/bdist.macosx-10.3-i386/egg/Cheetah/ErrorCatchers.py",
line 16,
in <module>
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-macosx-10.3-i386-ucs2/Cheetah-1
.0-py2.5-macosx-10.3-i386.egg/Cheetah/NameMapper.py",
line 146
SyntaxError: from __future__ imports must occur at the beginning of
the file
I am still a bit concerned by my path and python_path variables, but
it
doesn't look like this error is related to them. Any ideas? I'm
afraid I've
spent too much time on this alrady and if I can't find a decent
solution, I
will have to bag this pathwayfor a few more months.
Thanks for your time!
-Jake Biesinger
ADD COMMENT
• link
•
modified 10.7 years ago
by
Nate Coraor ♦ 3.2k
•
written
10.7 years ago by
Jacob Biesinger • 40
