localhost doesn't work

Question

[koalachesaosservare]

HI I'm a new user, so I don't know if this is the right place to describe this problem. My galaxy on localhost:8080 doesn't work. in the log file there is this....

"python path is: /usr/lib/galaxy-server/eggs/kombu-3.0.12-py2.7.egg, /usr/lib/galaxy-server/eggs/anyjson-0.3.3-py2.7.egg, /usr/lib/galaxy-server/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/amqp-1.4.3-py2.7.egg, /usr/lib/galaxy-server/eggs/pexpect-2.4-py2.7.egg, /usr/lib/galaxy-server/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/Babel-1.3-py2.7.egg, /usr/lib/galaxy-server/eggs/pytz-2013.9-py2.7.egg, /usr/lib/galaxy-server/eggs/Mako-0.4.1-py2.7.egg, /usr/lib/galaxy-server/eggs/WebHelpers-1.3-py2.7.egg, /usr/lib/galaxy-server/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/WebOb-0.8.5-py2.7.egg, /usr/lib/galaxy-server/eggs/Routes-1.12.3-py2.7.egg, /usr/lib/galaxy-server/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /usr/lib/galaxy-server/eggs/wchartype-0.1-py2.7.egg, /usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg, /usr/lib/galaxy-server/eggs/docutils-0.7-py2.7.egg, /usr/lib/galaxy-server/eggs/PasteDeploy-1.5.0-py2.7.egg, /usr/lib/galaxy-server/eggs/Paste-1.7.5.1-py2.7.egg, /usr/lib/galaxy-server/lib, /usr/lib/galaxy-server/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg, /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
tool_shed.tool_shed_registry DEBUG 2017-02-10 10:46:20,041 Loading references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2017-02-10 10:46:20,041 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2017-02-10 10:46:20,041 Loaded reference to tool shed: Galaxy test tool shed
galaxy.eggs WARNING 2017-02-10 10:46:20,478 Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
migrate.versioning.repository DEBUG 2017-02-10 10:46:20,524 Loading repository lib/galaxy/model/migrate..."

Moreover, if I try to do

sudo apt-get install galaxy-server-{all,tools-bl}
E: Unable to locate package galaxy-server-all
E: Unable to locate package galaxy-server-tools-b

l

I'm working on ubuntu-biolinux

thanks

[EagleEye]

You might get quicker response in https://biostar.usegalaxy.org

Answer 1

[ALchEmiXt]

For the last part of your question: Did you add the galaxy repository to your ubuntu repositories? Else the apt-get will not work.

Follow the instructions on getgalaxy.org and you should be fine. However, isn't biolinux preconfigured to run galaxy? Then you should browse the biolinux website.

Regular way which probably also works on biolinux: Go to the galaxy folder. run

git status
git pull

If you do not have a Galaxy repository yet or you do not want to update the existing instance, run:

git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git

[koalachesaosservare]

thank you. I've solved!

[ALchEmiXt]

ok great. You updated or pulled a new version? Please accept the answer as solved.