diff --git a/doc/source/admin/framework_dependencies.rst b/doc/source/admin/framework_dependencies.rst index 4c4c54d4f24..d0d293a1539 100644 --- a/doc/source/admin/framework_dependencies.rst +++ b/doc/source/admin/framework_dependencies.rst @@ -1,7 +1,7 @@ .. _framework-dependencies: -Galaxy Framework Dependencies -============================= +Framework Dependencies +====================== Galaxy is a large Python application with a long list of `Python module dependencies`_. As a result, the Galaxy developers have made significant effort @@ -84,7 +84,7 @@ live in ``/srv/galaxy/venv`` and the Galaxy source code has been cloned to ``/srv/galaxy/server``. .. code-block:: console - + $ virtualenv /srv/galaxy/venv New python executable in /srv/galaxy/venv/bin/python Installing setuptools, pip, wheel...done. @@ -100,12 +100,12 @@ yourself to set up Galaxy pip and the dependencies without creating a virtualenv using the ``--no-create-venv`` option: .. code-block:: console - + (venv)$ PYTHONPATH= sh /srv/galaxy/server/scripts/common_startup.sh --no-create-venv Ignoring indexes: https://pypi.python.org/simple Collecting pip Downloading https://wheels.galaxyproject.org/packages/pip-8.0.0+gx1-py2.py3-none-any.whl (1.2MB) - 100% |████████████████████████████████| 1.2MB 37.8MB/s + 100% |████████████████████████████████| 1.2MB 37.8MB/s Installing collected packages: pip Found existing installation: pip 7.1.2 Uninstalling pip-7.1.2: @@ -113,13 +113,13 @@ virtualenv using the ``--no-create-venv`` option: Successfully installed pip-8.0.0+gx1 Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-linux_x86_64.whl (1.7MB) - 100% |████████████████████████████████| 1.7MB 25.4MB/s + 100% |████████████████████████████████| 1.7MB 25.4MB/s ... Collecting pysam==0.8.3+gx1 (from -r requirements.txt (line 69)) Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.3+gx1-cp27-cp27mu-linux_x86_64.whl (7.4MB) - 100% |████████████████████████████████| 7.4MB 15.1MB/s + 100% |████████████████████████████████| 7.4MB 15.1MB/s Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, @@ -307,48 +307,48 @@ automatic fetching of pinned dependencies. The following NEW packages will be INSTALLED: - babel: 2.1.1-py27_0 - bioblend: 0.7.0-py27_0 - boto: 2.38.0-py27_0 + babel: 2.1.1-py27_0 + bioblend: 0.7.0-py27_0 + boto: 2.38.0-py27_0 bx-python: 0.7.3-np110py27_1 - cheetah: 2.4.4-py27_0 - decorator: 4.0.6-py27_0 - docutils: 0.12-py27_0 - ecdsa: 0.11-py27_0 - fabric: 1.10.2-py27_0 - libgfortran: 1.0-0 - mako: 1.0.3-py27_0 - markupsafe: 0.23-py27_0 - mercurial: 3.4.2-py27_0 - nose: 1.3.7-py27_0 - numpy: 1.10.2-py27_0 - openblas: 0.2.14-3 - openssl: 1.0.2e-0 - paramiko: 1.15.2-py27_0 - paste: 1.7.5.1-py27_0 - pastedeploy: 1.5.2-py27_1 - pip: 7.1.2-py27_0 - pycrypto: 2.6.1-py27_0 - python: 2.7.11-0 - pytz: 2015.7-py27_0 - pyyaml: 3.11-py27_1 - readline: 6.2-2 - repoze.lru: 0.6-py27_0 - requests: 2.9.1-py27_0 - requests-toolbelt: 0.5.0-py27_0 - routes: 2.2-py27_0 - setuptools: 19.2-py27_0 - six: 1.10.0-py27_0 - sqlalchemy: 1.0.11-py27_0 - sqlite: 3.9.2-0 - sqlparse: 0.1.18-py27_0 - tk: 8.5.18-0 - webob: 1.4.1-py27_0 - wheel: 0.26.0-py27_1 - yaml: 0.1.6-0 - zlib: 1.2.8-0 + cheetah: 2.4.4-py27_0 + decorator: 4.0.6-py27_0 + docutils: 0.12-py27_0 + ecdsa: 0.11-py27_0 + fabric: 1.10.2-py27_0 + libgfortran: 1.0-0 + mako: 1.0.3-py27_0 + markupsafe: 0.23-py27_0 + mercurial: 3.4.2-py27_0 + nose: 1.3.7-py27_0 + numpy: 1.10.2-py27_0 + openblas: 0.2.14-3 + openssl: 1.0.2e-0 + paramiko: 1.15.2-py27_0 + paste: 1.7.5.1-py27_0 + pastedeploy: 1.5.2-py27_1 + pip: 7.1.2-py27_0 + pycrypto: 2.6.1-py27_0 + python: 2.7.11-0 + pytz: 2015.7-py27_0 + pyyaml: 3.11-py27_1 + readline: 6.2-2 + repoze.lru: 0.6-py27_0 + requests: 2.9.1-py27_0 + requests-toolbelt: 0.5.0-py27_0 + routes: 2.2-py27_0 + setuptools: 19.2-py27_0 + six: 1.10.0-py27_0 + sqlalchemy: 1.0.11-py27_0 + sqlite: 3.9.2-0 + sqlparse: 0.1.18-py27_0 + tk: 8.5.18-0 + webob: 1.4.1-py27_0 + wheel: 0.26.0-py27_1 + yaml: 0.1.6-0 + zlib: 1.2.8-0 - Proceed ([y]/n)? + Proceed ([y]/n)? Fetching packages ... boto-2.38.0-py 100% |############################################| Time: 0:00:00 3.27 MB/s @@ -397,7 +397,7 @@ automatic fetching of pinned dependencies. Collecting WebHelpers (from -r lib/galaxy/dependencies/requirements.txt (line 15)) Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB) - 100% |████████████████████████████████| 151kB 55.7MB/s + 100% |████████████████████████████████| 151kB 55.7MB/s ... @@ -425,7 +425,7 @@ install uWSGI into Galaxy virtualenv (by default, ``.venv``) using pip, e.g.: (.venv)$ pip install uwsgi Collecting uwsgi Downloading uwsgi-2.0.12.tar.gz (784kB) - 100% |████████████████████████████████| 786kB 981kB/s + 100% |████████████████████████████████| 786kB 981kB/s Building wheels for collected packages: uwsgi Running setup.py bdist_wheel for uwsgi Stored in directory: /home/nate/.cache/pip/wheels/a4/7b/7c/8cbe2fe2c2b963173361cc18aa726f165dc4803effbb8195fc diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst index 572f1cf274f..552103c851b 100644 --- a/doc/source/admin/index.rst +++ b/doc/source/admin/index.rst @@ -11,4 +11,5 @@ This documentation is in the midst of being ported and unified based on resource dependency_resolvers conda_faq framework_dependencies + reports useful_scripts diff --git a/doc/source/admin/reports.md b/doc/source/admin/reports.md new file mode 100644 index 00000000000..dcec7a76bb9 --- /dev/null +++ b/doc/source/admin/reports.md @@ -0,0 +1,21 @@ +# Galaxy Reports + +Galaxy includes a report tool that is separate from the main process but which gives lots of potentially useful information about the usage of a Galaxy instance, for example the numbers of jobs that have been run each month, how much disk space each user is currently consuming and so on. + +## Setup on localhost + +The report tool takes its configuration settings from a file called reports.ini, which is located in the config subdirectory of the Galaxy distribution. + +Configuring the reports for your local setup is a case of: + +* Making a copy of `reports.ini.sample` called `reports.ini`. +* Editing the `database_connection` parameter to match the one in your `galaxy.ini` file +* Optionally, editing the `port` parameter (by default the tool uses port 9001) + +You should also set the 'salt' parameter `session_secret` if you intend to expose the reports via the web proxy (see below). + +Then you can start the report server using `sh run_reports.sh` and view the reports by pointing a web browser running on the same server to http://127.0.0.1:9001. If you'd like the report tool to persist between sessions then use `sh run_reports.sh --daemon` to run it as a background process. As with Galaxy itself, use `--stop-daemon` to halt the background process. (The log file is written to `reports_webapp.log` if you need to try and debug a problem.) + +## Expose Outside + +To make your reports available from outside of the localhost using NGINX proxy server you can check out the [blogpost](http://galacticengineer.blogspot.co.uk/2015/06/exposing-galaxy-reports-via-nginx-in.html) by Peter Briggs.