Add documentation how to avoid data modification by tools

doc/source/admin/index.rst

@@ -11,6 +11,7 @@ This documentation is in the midst of being ported and unified based on resource
    config
    config_logging
    production
+   security
    nginx
    apache
    scaling

doc/source/admin/security.md

@@ -0,0 +1,21 @@
+# Security considerations
+
+### Protect Galaxy against data loss due to misbehaving tools
+
+Tools have access to the paths of input and output data sets which are stored in
+``file_path`` and by default the credentials used for running tools are the same
+as for running Galaxy. Thus it is possible that a tool modifies data in Galaxy's
+``file_path``. Examples of such potential changes are:
+
+- Creation of additional files, e.g. indices, which is a problem for cleaning up data, because Galaxy does not know about these files.
+- Removal of tool input or output files. This will create problems with other tools using these datasets (note that most tool repositories use CI tests to to avoid this, but the problem may still occur).
+
+Note that a tool only knows the paths to its inputs and outputs, but if using the default configuration for other paths (e.g. the configuration directory) also these paths can be calculated and accessed.
+
+There are three approaches to protect Galaxy against these risks:
+
+- Use different credentials for running tools. This can be configured using the ``real_system_username`` config variable.
+- Configure Galaxy to run jobs in a container and enable ``outputs_to_working_directory``. Then the tool will execute in an environment that allows write access only for the job working dir. All other paths will be accessible read only. 
+- Use [Pulsar](https://pulsar.readthedocs.io/) to stage inputs and outputs.
+
+More information on pulsar configuration can be found in the [job configuration](jobs.md) documentation, and the other two are explained in [using a compute cluster](cluster.md).