Hello guys,

I’m still stuck on this error.

I’ve installed a brand new galaxy v16.01

And when I start it, I get the big error mentioned below.

Here’s the last message in the error:

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

Thanks for your assistance!

Cheers,

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

From: Fernandez Edgar
Sent: May-19-16 8:48 AM
To: 'galaxy-dev@bx.psu.edu' <galaxy-dev@bx.psu.edu>
Subject: RE: [galaxy-dev] not sure what I can do about this...

Hey Guys,

I’ve fixed my first problem with the environment.

But I’m still getting the second one.

Also, did any of you guys try to deploy galaxy with Microsoft Azure?

I’m actually looking into it and I was wondering if you had any input…

Let me know if you have any info on my libchtslib.so: input error or Microsoft Azure.

Cheers!

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

From: Fernandez Edgar
Sent: May-18-16 2:00 PM
To: galaxy-dev@bx.psu.edu
Subject: RE: [galaxy-dev] not sure what I can do about this...

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