Re: [galaxy-dev] More problems installing Galaxy
;
+ for rmfile in '$RMFILES'
+ '[' -f lib/pkg_resources.pyc ']'
+ : config/galaxy.ini
+ '[' '!' -f config/galaxy.ini ']'
+ '[' '!' -f config/galaxy.ini ']'
+ : .venv
+ '[' 1 -eq 1 -a 1 -eq 1 ']'
+ '[' '!' -d .venv ']'
+ '[' 1 -eq 1 ']'
+ '[' -d .venv ']'
+ printf 'Activating virtualenv at .venv\n'
Activating virtualenv at .venv
+ . .venv/bin/activate
++ deactivate nondestructive
++ unset pydoc
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/home/galaxy/galaxy/.venv
++ export VIRTUAL_ENV
++
_OLD_VIRTUAL_PATH=/usr/lib64/qt-3.3/bin:/usr/lib/jvm/java-openjdk/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/bin:/opt/env-switcher/bin
++
PATH=/home/galaxy/galaxy/.venv/bin:/usr/lib64/qt-3.3/bin:/usr/lib/jvm/java-openjdk/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/bin:/opt/env-switcher/bin
++ export PATH
++ '[' -n '' ']'
++ '[' -z '' ']'
++ _OLD_VIRTUAL_PS1=
++ '[' x '!=' x ']'
+++ basename /home/galaxy/galaxy/.venv
++ '[' .venv = __ ']'
+++ basename /home/galaxy/galaxy/.venv
++ PS1='(.venv)'
++ export PS1
++ alias 'pydoc=python -m pydoc'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
+ unset PYTHONPATH
+ '[' -z /home/galaxy/galaxy/.venv ']'
+ : https://wheels.galaxyproject.org/simple
+ '[' 1 -eq 1 ']'
+ /usr/local/bin/pip2.7 install 'pip>=8.1'
Traceback (most recent call last):
File "/usr/local/bin/pip2.7", line 5, in
from pkg_resources import load_entry_point
File
"/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py",
line 2850, in
working_set.require(__requires__)
File
"/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py",
line 696, in require
needed = self.resolve(parse_requirements(requirements))
File
"/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py",
line 594, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: pip==9.0.1
+ exit 1
Any suggestion?
I don't know where to go from here.
From: Dannon Baker
Sent: Wednesday, November 16, 2016 3:12 PM
To: Hernán Piqueras
Cc: Galaxy Dev List
Subject: Re: [galaxy-dev] More problems installing Galaxy
Hernan,
Sorry for the slow response here, have you made any progress? I'd be glad to
help sort this out.
Instead of creating an alias to a particular python in your .bashrc, I'd
recommend that if you're having problems you should manually create the
virtualenv with the specific python version you want. Once you've done that,
on galaxy's first start, it'll populate the requirements correctly.
An example command would be:
virtualenv -p /usr/local/bin/python2.7 .venv
Execute this command from the galaxy directory, and it'll create a virtualenv
named .venv, which is what Galaxy expects to use. After that, just start
Galaxy and the requirements should be installed to .venv automatically.
-Dannon
On Wed, Nov 9, 2016 at 2:39 PM, Hernán Piqueras
mailto:yj...@hotmail.com>> wrote:
I have a Linux with both Python 2.6 and Python 2.7. Apparently Python is so bad
designed that you cannot simply upgrade from 2.6 to 2.7 without breaking your
system. As latest Galaxy works with Python 2.7, I put an alias in my .bashrc to
/usr/local/bin/python2.7 and the same with virtualenv. I also enabled bash
debugging and enabled expanded alias into .sh scripts.
Then I ran :
$ sh galaxy/run.sh
... lots of output ---
Requirement already satisfied: pysam==0.8.4+gx1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70))
Requirement already satisfied: PasteScript in
./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r
requirements.txt (line 51))
++ PYTHONPATH=lib
++ /usr/local/bin/python2.7 -c 'import galaxy.dependencies; print
'\''\n'\''.join(galaxy.dependencies.optional('\''config/galaxy.ini'\''))'
Traceback (most recent call last):
File "", line 1, in
File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in
from galaxy.util import asbool
File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in
from six import binary_type, iteritems, PY3, string
Re: [galaxy-dev] More problems installing Galaxy
Hernan,
Sorry for the slow response here, have you made any progress? I'd be glad
to help sort this out.
Instead of creating an alias to a particular python in your .bashrc, I'd
recommend that if you're having problems you should manually create the
virtualenv with the specific python version you want. Once you've done
that, on galaxy's first start, it'll populate the requirements correctly.
An example command would be:
virtualenv -p /usr/local/bin/python2.7 .venv
Execute this command from the galaxy directory, and it'll create a
virtualenv named .venv, which is what Galaxy expects to use. After that,
just start Galaxy and the requirements should be installed to .venv
automatically.
-Dannon
On Wed, Nov 9, 2016 at 2:39 PM, Hernán Piqueras wrote:
> I have a Linux with both Python 2.6 and Python 2.7. Apparently Python is
> so bad designed that you cannot simply upgrade from 2.6 to 2.7 without
> breaking your system. As latest Galaxy works with Python 2.7, I put an
> alias in my .bashrc to /usr/local/bin/python2.7 and the same with
> virtualenv. I also enabled bash debugging and enabled expanded alias into
> .sh scripts.
>
>
> Then I ran :
>
>
> $ sh galaxy/run.sh
>
>
> ... lots of output ---
>
> Requirement already satisfied: pysam==0.8.4+gx1 in
> ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70))
> Requirement already satisfied: PasteScript in
> ./.venv/lib/python2.7/site-packages
> (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 51))
> ++ PYTHONPATH=lib
> ++ /usr/local/bin/python2.7 -c 'import galaxy.dependencies; print
> '\''\n'\''.join(galaxy.dependencies.optional('\''config/galaxy.ini'\''))'
> Traceback (most recent call last):
> File "", line 1, in
> File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9,
> in
> from galaxy.util import asbool
> File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in
>
> from six import binary_type, iteritems, PY3, string_types, text_type
> ImportError: No module named six
> + GALAXY_CONDITIONAL_DEPENDENCIES=
> + exit 1
>
>
> If I check with root user, six package is installed. My guess was I
> am missing an alias to pip2.7, then I added such alias in my .bashrc and
> again:
>
>
> $ sh galaxy/run.sh
>
>
> ... lots of output ---
>
> ++ '[' -n /bin/bash -o -n '' ']'
> ++ hash -r
> + unset PYTHONPATH
> + '[' -z /home/galaxy/galaxy/.venv ']'
> + : https://wheels.galaxyproject.org/simple
> + '[' 1 -eq 1 ']'
> + /usr/local/bin/pip2.7 install 'pip>=8.1'
> Traceback (most recent call last):
> File "/usr/local/bin/pip2.7", line 5, in
> from pkg_resources import load_entry_point
> File "/usr/local/lib/python2.7/site-packages/distribute-0.6.
> 44-py2.7.egg/pkg_resources.py", line 2850, in
> working_set.require(__requires__)
> File "/usr/local/lib/python2.7/site-packages/distribute-0.6.
> 44-py2.7.egg/pkg_resources.py", line 696, in require
> needed = self.resolve(parse_requirements(requirements))
> File "/usr/local/lib/python2.7/site-packages/distribute-0.6.
> 44-py2.7.egg/pkg_resources.py", line 594, in resolve
> raise DistributionNotFound(req)
> pkg_resources.DistributionNotFound: pip==9.0.1
>
> # pip --version
> pip 9.0.1 from /usr/local/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg
> (python 2.7)
> I have installed Python 2.7 and its tools (virtualenv, pip, etc) following
> official guidelines.
>
>
> How can install the missing dependecies?
>
>
>
>
> ___
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>
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>
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and other Galaxy lists, please use the interface at:
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