9:02 p.m.
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Nonetheless, when I run it, it says that some eggs are out of date.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
2:12 p.m.
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#U...
--nate
On Tue, Nov 19, 2013 at 4:02 PM, Cesar Rodriguez <
CESAR.RODRIGUEZSANCHEZ(a)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Nonetheless, when I run it, it says that some eggs are out of date.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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3:10 a.m.
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(a)bx.psu.edu>
Fecha: miércoles 20 de noviembre de 2013 08:12
Para: César Rodríguez Sánchez <cesar.rodriguezsanchez(a)ucr.ac.cr>
CC: <galaxy-dev(a)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(a)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
___________________________________________________________
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/
5:40 p.m.
On Thu, Nov 21, 2013 at 10:10 PM, Dr. César Rodríguez Sánchez
<CESAR.RODRIGUEZSANCHEZ(a)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(a)bx.psu.edu>
Fecha: miércoles 20 de noviembre de 2013 08:12
Para: César Rodríguez Sánchez <cesar.rodriguezsanchez(a)ucr.ac.cr>
CC: <galaxy-dev(a)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#U...
--nate
On Tue, Nov 19, 2013 at 4:02 PM, Cesar Rodriguez
<CESAR.RODRIGUEZSANCHEZ(a)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/
3322
days inactive
3366
days old
galaxy-dev@lists.galaxyproject.org
3 comments
3 participants
participants (3)
-
Cesar Rodriguez -
Dr. César Rodríguez Sánchez
-
Nate Coraor