Hey Guys,

Hope everyone is doing well.

So I’m back at galaxy v16.01

I’m having a small problem.

My python system version is 2.6.6

So I installed python version 2.7.8 from  Software Collection Library release 1.2 packages for Oracle Linux 6 (x86_64)

This means I need to source an environment before being about to use it.

So what I’ve created a file config/local_env.sh with:

# Source python27

export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}}

export LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH}

# For systemtap

export XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}}

# For pkg-config

export PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}}

These export comes directly with the installation of python 2.7.8 in the file /opt/rh/python27/enable.

But when I started my galaxy it didn’t stick.

I had to insert those exports into the file run.sh right before the following line:

./scripts/common_startup.sh $common_startup_args || exit 1

Any suggestions to make it work?

Also, I get this error :

Traceback (most recent call last):

  File "./scripts/paster.py", line 27, in <module>

    serve.run()

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1061, in run

    invoke(command, command_name, options, args[1:])

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke

    exit_code = runner.run(args)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 223, in run

    result = self.command()

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 639, in command

    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 295, in loadapp

    return loadobj(APP, uri, name=name, **kw)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj

    global_conf=global_conf)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext

    global_conf=global_conf)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig

    return loader.get_context(object_type, name, global_conf)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 506, in get_context

    section)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 565, in _context_from_explicit

    value = import_string(found_expr)

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string

    return pkg_resources.EntryPoint.parse("x=" + s).load(False)

  File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load

    entry = __import__(self.module_name, globals(),globals(), ['__name__'])

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5, in <module>

    from galaxy.webapps.galaxy.buildapp import app_factory

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>

    import galaxy.app

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module>

    from galaxy import config, jobs

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module>

    from galaxy import model, util

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module>

    import galaxy.datatypes.registry

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module>

    import tabular

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module>

    from galaxy.datatypes.sniff import get_headers

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module>

    from galaxy.datatypes.binary import Binary

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module>

    import pysam

  File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>

    from pysam.libchtslib import *

ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64

Removing PID file paster.pid

PLEASE HELP ME !

Best regards,

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568