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More problems installing Galaxy

marcelo_t
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 "<string>", line 1, in <module>
  File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in <module>
    from galaxy.util import asbool
  File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in <module>
    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 <module>
    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 <module>
    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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Re: More problems installing Galaxy

Dannon Baker-2
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 <[hidden email]> 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 "<string>", line 1, in <module>
  File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in <module>
    from galaxy.util import asbool
  File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in <module>
    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 <module>
    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 <module>
    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?




___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: More problems installing Galaxy

marcelo_t

Hi Dannon


Thank you for the response. I have tried your suggestion, if I unalias everything this is the output:


bash-4.1$ virtualenv -p /usr/local/bin/python2.7 .venv
Traceback (most recent call last):
  File "/usr/bin/virtualenv", line 7, in <module>
    from virtualenv import main
ImportError: No module named virtualenv


If I keep the alias, i.e.:


bash-4.1$ alias
alias easy_install='/usr/local/bin/easy_install-2.7'
alias pip='/usr/local/bin/pip2.7'
alias python='/usr/local/bin/python2.7'
alias virtualenv='/usr/local/bin/virtualenv-2.7'

then execute:

bash-4.1$ virtualenv -p /usr/local/bin/python2.7 .venv
Already using interpreter /usr/local/bin/python2.7
New python executable in .venv/bin/python2.7
Not overwriting existing python script .venv/bin/python (you must use .venv/bin/python2.7)
Installing setuptools.............done.
Installing pip...............done.

the output is pretty much the same as above:


bash-4.1$ sh galaxy/run.sh
+ shopt -s expand_aliases
+ source /home/galaxy/.bashrc
++ alias python=/usr/local/bin/python2.7
++ alias virtualenv=/usr/local/bin/virtualenv-2.7
++ alias pip=/usr/local/bin/pip2.7
++ alias easy_install=/usr/local/bin/easy_install-2.7
++ dirname galaxy/run.sh
+ cd galaxy
+ '[' -z '' ']'
+ GALAXY_LOCAL_ENV_FILE=./config/local_env.sh
+ '[' -f ./config/local_env.sh ']'
+ . ./config/local_env.sh
+ :
+ case "$1" in
+ break
+ ./scripts/common_startup.sh
+ shopt -s expand_aliases
+ source /home/galaxy/.bashrc
++ alias python=/usr/local/bin/python2.7
++ alias virtualenv=/usr/local/bin/virtualenv-2.7
++ alias pip=/usr/local/bin/pip2.7
++ alias easy_install=/usr/local/bin/easy_install-2.7
+ SET_VENV=1
+ /usr/local/bin/python2.7 -V
+ grep -q -e Anaconda -e 'Continuum Analytics'
+ CONDA_ALREADY_INSTALLED=0
+ DEV_WHEELS=0
+ FETCH_WHEELS=1
+ CREATE_VENV=1
+ REPLACE_PIP=1
+ COPY_SAMPLE_FILES=1
+ SAMPLES='
    config/migrated_tools_conf.xml.sample
    config/shed_tool_conf.xml.sample
    config/shed_tool_data_table_conf.xml.sample
    config/shed_data_manager_conf.xml.sample
    lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
    tool-data/shared/ucsc/builds.txt.sample
    tool-data/shared/ucsc/manual_builds.txt.sample
    tool-data/shared/ucsc/ucsc_build_sites.txt.sample
    tool-data/shared/igv/igv_build_sites.txt.sample
    tool-data/shared/rviewer/rviewer_build_sites.txt.sample
    static/welcome.html.sample
'
+ RMFILES='
    lib/pkg_resources.pyc
'
+ '[' 1 -eq 1 ']'
+ for sample in '$SAMPLES'
+ file=config/migrated_tools_conf.xml
+ '[' '!' -f config/migrated_tools_conf.xml -a -f config/migrated_tools_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=config/shed_tool_conf.xml
+ '[' '!' -f config/shed_tool_conf.xml -a -f config/shed_tool_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=config/shed_tool_data_table_conf.xml
+ '[' '!' -f config/shed_tool_data_table_conf.xml -a -f config/shed_tool_data_table_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=config/shed_data_manager_conf.xml
+ '[' '!' -f config/shed_data_manager_conf.xml -a -f config/shed_data_manager_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml
+ '[' '!' -f lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml -a -f lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/ucsc/builds.txt
+ '[' '!' -f tool-data/shared/ucsc/builds.txt -a -f tool-data/shared/ucsc/builds.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/ucsc/manual_builds.txt
+ '[' '!' -f tool-data/shared/ucsc/manual_builds.txt -a -f tool-data/shared/ucsc/manual_builds.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/ucsc/ucsc_build_sites.txt
+ '[' '!' -f tool-data/shared/ucsc/ucsc_build_sites.txt -a -f tool-data/shared/ucsc/ucsc_build_sites.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/igv/igv_build_sites.txt
+ '[' '!' -f tool-data/shared/igv/igv_build_sites.txt -a -f tool-data/shared/igv/igv_build_sites.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/rviewer/rviewer_build_sites.txt
+ '[' '!' -f tool-data/shared/rviewer/rviewer_build_sites.txt -a -f tool-data/shared/rviewer/rviewer_build_sites.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=static/welcome.html
+ '[' '!' -f static/welcome.html -a -f static/welcome.html.sample ']'
+ 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 <module>
    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 <module>
    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 <[hidden email]>
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 <[hidden email]> 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 "<string>", line 1, in <module>
  File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in <module>
    from galaxy.util import asbool
  File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in <module>
    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 <module>
    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 <module>
    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?




___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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