Hi there, I am trying to install Galaxy locally on my Mac OSX 10.9, python 2.7. Nonetheless, when I run it, it says that some eggs are out of date. I have fetched them, but the following message appears: Mac-Pro-Cesar-Rodriguez:scripts Rodriguez$ python fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "paramiko" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/Rodriguez/galaxy-dist/lib/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (paramiko 1.11.1 (/Users/Rodriguez/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4¹)) What should I do to fix this? Thank you so much for your help. Cesar
Hi Cesar, The easiest way to avoid module version conflicts is to use virtualenv to set up a self-contained environment: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_... --nate On Tue, Nov 19, 2013 at 4:02 PM, Cesar Rodriguez < CESAR.RODRIGUEZSANCHEZ@ucr.ac.cr> wrote:
Hi there, I am trying to install Galaxy locally on my Mac OSX 10.9, python 2.7. Nonetheless, when I run it, it says that some eggs are out of date. I have fetched them, but the following message appears:
Mac-Pro-Cesar-Rodriguez:scripts Rodriguez$ python fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution.
Dependency "paramiko" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
File "fetch_eggs.py", line 37, in <module>
c.resolve() # Only fetch eggs required by the config
File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve
egg.resolve()
File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve
dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch )
File "/Users/Rodriguez/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1 (/Users/Rodriguez/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4’))
What should I do to fix this?
Thank you so much for your help.
Cesar
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Dear Nate, I am trying to install galaxy on a different computer. This time it does not run because of the following: Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string File "/Users/rodriguez/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/rodriguez/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <module> File "/Users/rodriguez/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 40, in <module> File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/support.py", line 29, in <module> File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/dates.py", line 34, in <module> File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/core.py", line 642, in default_locale File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/core.py", line 763, in parse_locale ValueError: expected only letters, got 'utf-8' How can I solve this locale issue? Thanks Cesar De: Nate Coraor <nate@bx.psu.edu> Fecha: miércoles 20 de noviembre de 2013 08:12 Para: César Rodríguez Sánchez <cesar.rodriguezsanchez@ucr.ac.cr> CC: <galaxy-dev@bx.psu.edu> Asunto: Re: [galaxy-dev] Local installation problem Hi Cesar, The easiest way to avoid module version conflicts is to use virtualenv to set up a self-contained environment: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_ a_clean_environment --nate On Tue, Nov 19, 2013 at 4:02 PM, Cesar Rodriguez <CESAR.RODRIGUEZSANCHEZ@ucr.ac.cr> wrote:
Hi there, I am trying to install Galaxy locally on my Mac OSX 10.9, python 2.7. Nonetheless, when I run it, it says that some eggs are out of date. I have fetched them, but the following message appears:
Mac-Pro-Cesar-Rodriguez:scripts Rodriguez$ python fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution.
Dependency "paramiko" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
File "fetch_eggs.py", line 37, in <module>
c.resolve() # Only fetch eggs required by the config
File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve
egg.resolve()
File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve
dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch )
File "/Users/Rodriguez/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1 (/Users/Rodriguez/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4¹))
What should I do to fix this?
Thank you so much for your help.
Cesar
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On Thu, Nov 21, 2013 at 10:10 PM, Dr. César Rodríguez Sánchez <CESAR.RODRIGUEZSANCHEZ@ucr.ac.cr> wrote:
Dear Nate, I am trying to install galaxy on a different computer. This time it does not run because of the following:
Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit File "/Users/rodriguez/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string File "/Users/rodriguez/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/rodriguez/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <module> File "/Users/rodriguez/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 40, in <module> File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/support.py", line 29, in <module> File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/dates.py", line 34, in <module> File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/core.py", line 642, in default_locale File "/Users/rodriguez/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg/babel/core.py", line 763, in parse_locale ValueError: expected only letters, got 'utf-8'
How can I solve this locale issue?
Hi Cesar, Sorry I didn't get back to you earlier. If you haven't yet discovered the solution, this is occurring because of a bug in the version of the Babel library Galaxy is using. To work around this, set the environment variable `LC_ALL` to a valid locale, e.g. 'en_US.UTF-8' or 'C', before starting Galaxy: % export LC_ALL='en_US.UTF-8' % sh run.sh --nate
Thanks Cesar De: Nate Coraor <nate@bx.psu.edu> Fecha: miércoles 20 de noviembre de 2013 08:12 Para: César Rodríguez Sánchez <cesar.rodriguezsanchez@ucr.ac.cr> CC: <galaxy-dev@bx.psu.edu> Asunto: Re: [galaxy-dev] Local installation problem
Hi Cesar,
The easiest way to avoid module version conflicts is to use virtualenv to set up a self-contained environment:
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_...
--nate
On Tue, Nov 19, 2013 at 4:02 PM, Cesar Rodriguez <CESAR.RODRIGUEZSANCHEZ@ucr.ac.cr> wrote:
Hi there, I am trying to install Galaxy locally on my Mac OSX 10.9, python 2.7. Nonetheless, when I run it, it says that some eggs are out of date. I have fetched them, but the following message appears:
Mac-Pro-Cesar-Rodriguez:scripts Rodriguez$ python fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution.
Dependency "paramiko" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
File "fetch_eggs.py", line 37, in <module>
c.resolve() # Only fetch eggs required by the config
File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve
egg.resolve()
File "/Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve
dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch )
File "/Users/Rodriguez/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1 (/Users/Rodriguez/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4’))
What should I do to fix this?
Thank you so much for your help.
Cesar
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Cesar Rodriguez -
Dr. César Rodríguez Sánchez
-
Nate Coraor