Question: Problem Using Galaxy
0
Seyed Mehdi Jazayeri • 10 wrote:
Dear Sir/Madam,
I am a PhD student working on RNA-Seq as my dissertation. As a matter
of
fact I want to do analyses of gene expressions for the sequences that
I
have and for that I have tried to use Galaxy tools as it is one of the
best
platforms in order to do analysis for RNA-Seq as well as others. I did
all
about installation of Galaxy on my Mac OS 10.7 Lion but when I run the
commands I do not get any result from running any type of commands.
And
when I do *run.sh *I will have nothing done. As a sample I send you
the
command I ran on my system as follow
*
*
*iMac-de-Biologia:galaxy-dist LabBioMol$ ./run.sh*
*Traceback (most recent call last):*
* File "./scripts/paster.py", line 34, in <module>*
* command.run()*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 84, in run*
* invoke(command, command_name, options, args[1:])*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 123, in invoke*
* exit_code = runner.run(args)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 218, in run*
* result = self.command()*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 276, in command*
* relative_to=base, global_conf=vars)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 313, in loadapp*
* **kw)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp*
* return loadobj(APP, uri, name=name, **kw)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj*
* global_conf=global_conf)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext*
* global_conf=global_conf)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig*
* return loader.get_context(object_type, name, global_conf)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 413, in get_context*
* section)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 458, in _context_from_explicit*
* value = import_string(found_expr)*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 18, in import_string*
* return pkg_resources.EntryPoint.parse("x="+s).load(False)*
* File "/Users/LabBioMol/galaxy-python/galaxy-
dist/lib/pkg_resources.py",
line 1954, in load*
* entry = __import__(self.module_name, globals(),globals(),
['__name__'])
*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/lib/galaxy/web/__init__.py",
line 5, in <module>*
* from framework import expose, json, json_pretty, require_login,
require_admin, url_for, error, form, FormBuilder, expose_api*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/lib/galaxy/web/framework/__init__.py",
line 31, in <module>*
* from babel.support import Translations*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/Babel-0.9.4-py2.7.egg/babel/support.py",
line 29, in <module>*
* from babel.dates import format_date, format_datetime,
format_time,
LC_TIME*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py",
line 34, in <module>*
* LC_TIME = default_locale('LC_TIME')*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py",
line 642, in default_locale*
* return '_'.join(filter(None, parse_locale(locale)))*
* File
"/Users/LabBioMol/galaxy-python/galaxy-
dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py",
line 763, in parse_locale*
* raise ValueError('expected only letters, got %r' % lang)*
*ValueError: expected only letters, got 'utf-8'*
*iMac-de-Biologia:galaxy-dist LabBioMol$ *
Now I would appreciate if you could advise me what is the problem and
how
to solve it.
Thanks for your attention in advance.
Best regards
SMJ
--
SMJ
Seyed Mehdi Jazayeri
ADD COMMENT
• link
•
modified 6.5 years ago
by
Nate Coraor ♦ 3.2k
•
written
6.5 years ago by
Seyed Mehdi Jazayeri • 10
