Re: [galaxy-dev] Problem starting toolshed
An extension on the problem to get Toolshed to start.
On my 'sandbox' machine, I can launch toolshed now.
But on our test-production, running run_community.sh now still fails,
complaining mercurial is not installed.
But on this system (Centos5), I have problems to install mercurial for
Python version 2.6
- I simply did what I have done on my sandbox machine, but no avail. Then...
- I have set PYTHONPATH to /opt/Python-2.6.6
- # python -Voutputs Python 2.6.6
- # python /usr/bin/easy_install --prefix /opt/Python-2.6.6 -U mercurial
Traceback (most recent call last):
File "/usr/bin/easy_install", line 5, in
from pkg_resources import load_entry_point
ImportError: No module named pkg_resources
However, I have reinstalled python-setuptools (which provides
pkg_resources), but no luck.
I hope somebody can guide me a bit further?
Kind regards,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/23/2012 04:07 PM, Joachim Jacob wrote:
Thanks for your fast reply! It did the trick and kept me going on a
sunny friday afternoon. :-)
# easy_install -U mercurial
Cheers,
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/23/2012 03:47 PM, Greg Von Kuster wrote:
You'll need to configure your Python 2.6 to include mercurial. You
can do something like
easy_install -U mercurial
but there are other approaches as well.
On Mar 23, 2012, at 10:33 AM, Joachim Jacob wrote:
Hi all,
In order to ease sharing the developed Galaxy tools in our group, we
want to launch a private Toolshed.
However, upon running ./run_community.sh, I got following error.
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in
command.run()
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run
result = self.command()
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 276, in command
relative_to=base, global_conf=vars)
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 313, in loadapp
**kw)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 413, in get_context
section)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 458, in _context_from_explicit
value = import_string(found_expr)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/home/galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in
load
entry = __import__(self.module_name, globals(),globals(),
['__name__'])
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/community/buildapp.py",
line 16, in
import galaxy.webapps.community.model
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/community/model/__init__.py",
line 12, in
from mercurial import hg, ui
ImportError: No module named mercurial
Removing PID file community_webapp.pid
What I understand, there is a conflict between Python2.6 (manually
installed under /opt) and Python2.4 (system-wide version). In
version 2.6, I do not have mercurial available apparently.
Any hint about a fix?
Kind regards,
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
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Re: [galaxy-dev] Problem starting toolshed
Thanks for your fast reply! It did the trick and kept me going on a
sunny friday afternoon. :-)
# easy_install -U mercurial
Cheers,
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/23/2012 03:47 PM, Greg Von Kuster wrote:
You'll need to configure your Python 2.6 to include mercurial. You
can do something like
easy_install -U mercurial
but there are other approaches as well.
On Mar 23, 2012, at 10:33 AM, Joachim Jacob wrote:
Hi all,
In order to ease sharing the developed Galaxy tools in our group, we
want to launch a private Toolshed.
However, upon running ./run_community.sh, I got following error.
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in
command.run()
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run
result = self.command()
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 276, in command
relative_to=base, global_conf=vars)
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 313, in loadapp
**kw)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 413, in get_context
section)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 458, in _context_from_explicit
value = import_string(found_expr)
File
"/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/home/galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load
entry = __import__(self.module_name, globals(),globals(),
['__name__'])
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/community/buildapp.py",
line 16, in
import galaxy.webapps.community.model
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/community/model/__init__.py",
line 12, in
from mercurial import hg, ui
ImportError: No module named mercurial
Removing PID file community_webapp.pid
What I understand, there is a conflict between Python2.6 (manually
installed under /opt) and Python2.4 (system-wide version). In version
2.6, I do not have mercurial available apparently.
Any hint about a fix?
Kind regards,
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
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Re: [galaxy-dev] Problem starting toolshed
You'll need to configure your Python 2.6 to include mercurial. You can do
something like
easy_install -U mercurial
but there are other approaches as well.
On Mar 23, 2012, at 10:33 AM, Joachim Jacob wrote:
> Hi all,
>
>
> In order to ease sharing the developed Galaxy tools in our group, we want to
> launch a private Toolshed.
>
> However, upon running ./run_community.sh, I got following error.
>
> Traceback (most recent call last):
> File "./scripts/paster.py", line 34, in
>command.run()
> File
> "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
> line 84, in run
>invoke(command, command_name, options, args[1:])
> File
> "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
> line 123, in invoke
>exit_code = runner.run(args)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
> line 218, in run
>result = self.command()
> File
> "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
> line 276, in command
>relative_to=base, global_conf=vars)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
> line 313, in loadapp
>**kw)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 204, in loadapp
>return loadobj(APP, uri, name=name, **kw)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 224, in loadobj
>global_conf=global_conf)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 248, in loadcontext
>global_conf=global_conf)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 278, in _loadconfig
>return loader.get_context(object_type, name, global_conf)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 413, in get_context
>section)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 458, in _context_from_explicit
>value = import_string(found_expr)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 18, in import_string
>return pkg_resources.EntryPoint.parse("x="+s).load(False)
> File "/home/galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load
>entry = __import__(self.module_name, globals(),globals(), ['__name__'])
> File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/community/buildapp.py",
> line 16, in
>import galaxy.webapps.community.model
> File
> "/home/galaxy/galaxy-dist/lib/galaxy/webapps/community/model/__init__.py",
> line 12, in
>from mercurial import hg, ui
> ImportError: No module named mercurial
> Removing PID file community_webapp.pid
>
> What I understand, there is a conflict between Python2.6 (manually installed
> under /opt) and Python2.4 (system-wide version). In version 2.6, I do not
> have mercurial available apparently.
>
> Any hint about a fix?
>
>
> Kind regards,
> Joachim
>
> --
> Joachim Jacob, PhD
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
>
> ___
> 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/
___
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/
