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 <dannon.baker@gmail.com>
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