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add basic Reports documentation

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This commit is contained in:
Martin Cech
2017-03-27 15:39:54 -04:00
parent b4feb85f11
commit bdcf4807ce
3 changed files with 71 additions and 49 deletions
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doc/source/admin/framework_dependencies.rst
+49 -49
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@@ -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
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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
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...
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
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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
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...
@@ -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
doc/source/admin/index.rst
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@@ -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
doc/source/admin/reports.md
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@@ -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.