Question: Problem Using Galaxy
gravatar for Seyed Mehdi Jazayeri
6.5 years ago by
France, Montpellier
Seyed Mehdi Jazayeri10 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 * *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$ ./* *Traceback (most recent call last):* * File "./scripts/", line 34, in <module>* ** * File "/Users/LabBioMol/galaxy-python/galaxy- dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/", 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/", line 123, in invoke* * exit_code =* * File "/Users/LabBioMol/galaxy-python/galaxy- dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/", line 218, in run* * result = self.command()* * File "/Users/LabBioMol/galaxy-python/galaxy- dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/", 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/", line 313, in loadapp* * **kw)* * File "/Users/LabBioMol/galaxy-python/galaxy- dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/", 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/", 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/", 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/", 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/", line 413, in get_context* * section)* * File "/Users/LabBioMol/galaxy-python/galaxy- dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/", 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/", line 18, in import_string* * return pkg_resources.EntryPoint.parse("x="+s).load(False)* * File "/Users/LabBioMol/galaxy-python/galaxy- dist/lib/", line 1954, in load* * entry = __import__(self.module_name, globals(),globals(), ['__name__']) * * File "/Users/LabBioMol/galaxy-python/galaxy- dist/lib/galaxy/web/", 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/", line 31, in <module>* * from import Translations* * File "/Users/LabBioMol/galaxy-python/galaxy- dist/eggs/Babel-0.9.4-py2.7.egg/babel/", 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/", 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/", 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/", 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
galaxy • 1.1k views
ADD COMMENTlink modified 6.5 years ago by Nate Coraor3.2k • written 6.5 years ago by Seyed Mehdi Jazayeri10
gravatar for Nate Coraor
6.5 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:
Hi, Please try starting with: $ LC_ALL=C ./ --nate
ADD COMMENTlink written 6.5 years ago by Nate Coraor3.2k

Hi, Thanks a lot. It was of help and solved the problem.

ADD REPLYlink written 4 weeks ago by Seyed Mehdi Jazayeri10
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