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)<https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149> 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
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