======================
Scipion for facilities
======================
+------------------+------------------+
| stable: |stable| | devel: |devel| |
+------------------+------------------+
.. |stable| image:: http://scipion-test.cnb.csic.es:9980/badges/facilities_prod.svg
.. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/facilities_sdevel.svg
'scipion-em-facilities' plugin allows to use different utils for cryo-EM facilities
(like monitors) within the Scipion framework.
Monitors are used to produce live analysis plots, generate reports or
raise alerts when some problems are detected. A monitor example is the CTF-monitor,
that checks the computed defocus values for each micrograph as they are generated.
CTF-monitor may raise an alert if the defocus values are above or below certain thresholds.
A special case of this monitors is the monitor summary which encapsulates the CTF Monitor,
the system monitor and the movie gain monitor and continuously creates a report.
This module contains protocols and utilities related with monitors.
Please, check the `facilities documentation <https://scipion-em.github.io/docs/docs/facilities/facilities.html>`_
for more details.
Installation
------------
You will need to use `Scipion 3.0 <https://scipion-em.github.io/docs/release-3.0.0/index.html>`_
to be able to run these protocols. If you want to use the summary monitor with grafana
you will need to create the file secrets.cfg in the directory defined by the variable EMFACILITIES_HOME
(see the above mention web site for details).
To install the plugin, you have two options:
a) Stable version
.. code-block::
scipion3 installp -p scipion-em-facilities
b) Developer's version
* 1st. Download repository
.. code-block::
git clone https://github.com/scipion-em/scipion-em-facilities.git /path/to/scipion-em-facilities
* 2nd. Install the plugin
.. code-block::
scipion3 installp -p /path/to/scipion-em-facilities --devel
Testing
-------
To check the installation, simply run the following Scipion test:
.. code-block::
scipion3 test --grep emfacilities --mode modules --run
If ``--run`` is not passed, it only shows the available tests to check.
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"description": "======================\nScipion for facilities\n======================\n\n+------------------+------------------+\n| stable: |stable| | devel: |devel| |\n+------------------+------------------+\n\n.. |stable| image:: http://scipion-test.cnb.csic.es:9980/badges/facilities_prod.svg\n.. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/facilities_sdevel.svg\n\n'scipion-em-facilities' plugin allows to use different utils for cryo-EM facilities\n(like monitors) within the Scipion framework.\n\nMonitors are used to produce live analysis plots, generate reports or\nraise alerts when some problems are detected. A monitor example is the CTF-monitor,\nthat checks the computed defocus values for each micrograph as they are generated.\nCTF-monitor may raise an alert if the defocus values are above or below certain thresholds.\nA special case of this monitors is the monitor summary which encapsulates the CTF Monitor,\nthe system monitor and the movie gain monitor and continuously creates a report.\n\nThis module contains protocols and utilities related with monitors.\n\nPlease, check the `facilities documentation <https://scipion-em.github.io/docs/docs/facilities/facilities.html>`_\nfor more details.\n\n\nInstallation\n------------\n\nYou will need to use `Scipion 3.0 <https://scipion-em.github.io/docs/release-3.0.0/index.html>`_\nto be able to run these protocols. If you want to use the summary monitor with grafana\nyou will need to create the file secrets.cfg in the directory defined by the variable EMFACILITIES_HOME\n(see the above mention web site for details).\n\nTo install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion3 installp -p scipion-em-facilities\n\nb) Developer's version\n\n * 1st. Download repository\n\n .. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-facilities.git /path/to/scipion-em-facilities\n\n * 2nd. Install the plugin\n\n .. code-block::\n\n scipion3 installp -p /path/to/scipion-em-facilities --devel\n\nTesting\n-------\n\nTo check the installation, simply run the following Scipion test:\n\n.. code-block::\n\n scipion3 test --grep emfacilities --mode modules --run\n\nIf ``--run`` is not passed, it only shows the available tests to check.\n\n\n",
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