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.egg/paste/debug/prints.py', line 98 in __call__ File '/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/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.egg/paste/recursive.py', line 80 in __call__ File '/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/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_runner.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-noplatform:/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/PAML/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-py2.5.egg/paste/script/command.py", line 78, in run File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 117, in invoke File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 212, in run File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 227, in command File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 250, in loadapp File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 213, in loadobj File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 237, in loadcontext File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 267, in _loadconfig File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 397, in get_context File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 439, in _context_from_explicit File "/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.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
Hi Jake, Jacob Biesinger wrote:
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
Python 2.5 on OS X Intel is a supported platform, but it looks like your Python isn't Universal (it doesn't support dual architectures). Which version of OS X are you using, and which Python (MacPorts)? For 10.4, MacPython is recommended: http://www.macpython.org/packages/ For 10.5, the system Python should work, but this has not been tested. If you stick with your current single-arch python, that's fine, but you won't have the benefit of pre-scrambled eggs (ours are for universal python only).
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.
Can you provide the error you got from scramble? pysqlite scrambles out of the box for me on an Intel Mac, but I'm not using the same python as you.
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:
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)
Our templates aren't currently Cheetah 2.x compatible. This is a strange problem, though, as paths in your $PYTHONPATH (which is set by the init scripts) should be placed at the beginning of sys.path, thus, our eggs should override your local modules. I have seen this happen with a few other people as well, but I can't duplicate it myself.
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 have a fix for this which I've just committed in rev 2514. Please update your copy of Galaxy and scramble Cheetah again. --nate
participants (2)
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Jacob Biesinger -
Nate Coraor