How to uninstall local Galaxy

Question: How to uninstall local Galaxy

3.4 years ago by

United States

I have installed galaxy using git on a local linux PC wiki.galaxyproject.org/Admin/GetGalaxy) Unfortunately, I am running out of space on that hard drive. I tried to install galaxy using the same commands on other hard drives, but that wouldn't work. Any ideas on how to move the galaxy folder and its dependencies or how to de-install it completely and install galaxy form scratch elsewhere?

Thank you very much!

galaxy local • 1.6k views

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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by catic.andre • 0

Regarding uninstalling: Have you tried just deleting the whole folder where galaxy is installed?

As far as I know, the installation on Linux only uses one folder. If you want to change which hard drive galaxy is intalled on, you could try to just move that folder to the new hard drive on the same computer. However, if you want to move to another computer, you should just do a fresh install on that new computer.

ADD REPLY • link written 3.4 years ago by ivar.grytten • 50

3.3 years ago by

catic.andre • 0

United States

catic.andre • 0 wrote:

I have now removed the original galaxy installation and installed again on another drive. This is what I see when I execute run.sh:

run.sh:28: run.sh: ./scripts/common_startup.sh: Permission denied

Traceback (most recent call last):
File "./scripts/paster.py", line 37, in <module>
serve.run()
File "/media/andre/DATA/galaxy/lib/

galaxy/util/pastescript/serve.py", line 1049, in run
    invoke(command, command_name, options, args[1:])
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke
    exit_code = runner.run(args)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/serve.py", line 220, in run
    result = self.command()
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/serve.py", line 641, in command
    server = loadserver(server_spec, name=server_name, relative_to=base, global_conf=vars)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 358, in loadserver
    return loadobj(SERVER, uri, name=name, **kw)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj
    global_conf=global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext
    global_conf=global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig
    return loader.get_context(object_type, name, global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 557, in get_context
    section)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 579, in _context_from_use
    object_type, name=use, global_conf=global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 509, in get_context
    global_conf=global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext
    global_conf=global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 431, in _loadegg
    return loader.get_context(object_type, name, global_conf)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 723, in get_context
    object_type, name=name)
File "/media/andre/DATA/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 762, in find_egg_entry_point
    for prot in protocol_options] or '(no entry points)'))))
LookupError: Entry point 'http' not found in egg 'Paste' (dir: /media/andre/DATA/galaxy/eggs/Paste-1.7.5.1-py2.7.egg; protocols: paste.server_factory, paste.server_runner; entry_points: )

I can move the galaxy folder within the main OS drive, but when I copy it to another drive I'm out of luck. Any thoughts? Does the name of the auxiliary hard drives matter (they are all called "DATA")?
Thank you!

ADD COMMENT • link written 3.3 years ago by catic.andre • 0

You get a Permission denied error. Have you tried running the command as root, using "sudo sh run.sh"?

Please reply as a comment, not as a new anwer :)

ADD REPLY • link written 3.3 years ago by ivar.grytten • 50

Thank you, but the SUDO command did not change the outcome. This is the report I get from running a newly installed galaxy on an auxiliary drive:

andre@andre-Precision-Tower-5810:/media/andre/DATA/galaxy$ sudo sh run.sh
[sudo] password for andre:
run.sh: 28: run.sh: ./scripts/common_startup.sh: Permission denied
python path is: /media/andre/DATA/galaxy/eggs/Babel-1.3-py2.7.egg, /media/andre/DATA/galaxy/eggs/pytz-2013.9-py2.7.egg, /media/andre/DATA/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/Mako-0.4.1-py2.7.egg, /media/andre/DATA/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/kombu-3.0.24-py2.7.egg, /media/andre/DATA/galaxy/eggs/anyjson-0.3.3-py2.7.egg, /media/andre/DATA/galaxy/eggs/PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/WebHelpers-1.3-py2.7.egg, /media/andre/DATA/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg, /media/andre/DATA/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /media/andre/DATA/galaxy/eggs/Routes-2.1-py2.7.egg, /media/andre/DATA/galaxy/eggs/repoze.lru-0.6-py2.7.egg, /media/andre/DATA/galaxy/eggs/amqp-1.4.6-py2.7.egg, /media/andre/DATA/galaxy/eggs/pexpect-2.4-py2.7.egg, /media/andre/DATA/galaxy/eggs/wchartype-0.1-py2.7.egg, /media/andre/DATA/galaxy/eggs/docutils-0.7-py2.7.egg, /media/andre/DATA/galaxy/eggs/PasteDeploy-1.5.0-py2.7.egg, /media/andre/DATA/galaxy/eggs/Paste-1.7.5.1-py2.7.egg, /media/andre/DATA/galaxy/lib, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /usr/local/lib/python2.7/dist-packages, /usr/lib/python2.7/dist-packages/PILcompat, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/pymodules/python2.7, /usr/lib/python2.7/dist-packages/ubuntu-sso-client, /usr/lib/python2.7/dist-packages
Traceback (most recent call last):
File "/media/andre/DATA/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 51, in app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
File "/media/andre/DATA/galaxy/lib/galaxy/app.py", line 38, in __init__
    self.config.check()
File "/media/andre/DATA/galaxy/lib/galaxy/config.py", line 625, in check
    raise ConfigurationError("Tool config file not found: %s" % path )
ConfigurationError: Tool config file not found: ./config/shed_tool_conf.xml

Any ideas?

Many thanks!

ADD REPLY • link written 3.3 years ago by catic.andre • 0

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