DOC: Remove the destination paths in container documentation (#621)

* DOC: Remove the destination paths in container documentation

Remove the destination paths for the input and output binding input
arguments in the `Docker` and `Singularity` container usage instructions.

Avoids, for example, errors that mean that no (BIDS) data was
effectively found, e.g.:
```
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 833, in build_qsiprep_workflow
    layout = BIDSLayout(
  File "/usr/local/miniconda/lib/python3.8/site-packages/bids/layout/layout.py", line 135, in __init__
    root, description = validate_root(root, validate)
  File "/usr/local/miniconda/lib/python3.8/site-packages/bids/layout/validation.py", line 70, in validate_root
    raise ValueError("BIDS root does not exist: %s" % root)
ValueError: BIDS root does not exist: /mnt/data/my/path/
```

* make sure paths reflect the mount points

---------

Co-authored-by: Matt Cieslak <mattcieslak@gmail.com>

docs/installation.rst

@@ -21,51 +21,57 @@ Docker Container
 In order to run qsiprep in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
 Once Docker is installed, the recommended way to run qsiprep is to use the
-``qsiprep-docker`` wrapper, which requires Python and an Internet connection.
+``qsiprep-docker`` wrapper, which requires Python and an Internet connection
+and that you install the ``qsiprep-container`` package with ``pip``.
 
-.. note:: If running Docker Desktop on MacOS, be sure to set the memory to 6 or more GB.
-    Too little memory assigned to Docker Desktop can result in a message like ``Killed.``
+.. note:: If running Docker Desktop on MacOS (or via Docker Desktop), be sure to set
+    the memory to 6 or more GB. Too little memory assigned to Docker Desktop can result
+    in a message like ``Killed.``
 
 When run, ``qsiprep-docker`` will generate a Docker command line for you,
 print it out for reporting purposes, and then run the command, e.g.::
 
     $ qsiprep-docker /path/to/data/dir /path/to/output/dir participant
-    RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
-        -v /path/to_output/dir:/out pennbbl/qsiprep:1.0.0 \
+    RUNNING: docker run --rm -it -v /path/to/data/dir:/data \
+        -v /path/to_output/dir:/out pennbbl/qsiprep:latest \
         /data /out participant
     ...
 
 You may also invoke ``docker`` directly::
 
     $ docker run -ti --rm \
-        -v filepath/to/data/dir:/data:ro \
-        -v filepath/to/output/dir:/out \
+        -v /filepath/to/data/dir \
+        -v /filepath/to/output/dir \
+        -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
         pennbbl/qsiprep:latest \
-        /data /out participant
+        /filepath/to/data/dir /filepath/to/output/dir participant \
+        --fs-license-file /opt/freesurfer/license.txt
 
 For example: ::
 
     $ docker run -ti --rm \
-        -v $HOME/fullds005:/data:ro \
-        -v $HOME/dockerout:/out \
+        -v $HOME/fullds005 \
+        -v $HOME/dockerout \
+        -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
         pennbbl/qsiprep:latest \
-        /data /out participant \
-        --ignore fieldmaps
+        $HOME/fullds005 $HOME/dockerout participant \
+        --ignore fieldmaps \
+        --fs-license-file /opt/freesurfer/license.txt
 
-If you are running Freesurfer as part of QSIPrep, 
+If you are running Freesurfer as part of QSIPrep,
 you will need to mount your Freesurfer license.txt file when invoking ``docker`` ::
 
     $ docker run -ti --rm \
-        -v $HOME/fullds005:/data:ro \
-        -v $HOME/dockerout:/out \
+        -v $HOME/fullds005 \
+        -v $HOME/dockerout \
         -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
         pennbbl/qsiprep:latest \
-        /data /out participant \
+        $HOME/fullds005 -v $HOME/dockerout participant \
         --fs-license-file /opt/freesurfer/license.txt
 
 
-See `External Dependencies`_ for more information (e.g., specific versions) on
-what is included in the latest Docker images.
+See `External Dependencies`_ for more information on what is included in the Docker image
+and how it's built.
 
 
 
@@ -77,28 +83,22 @@ The easiest way to get a Sigularity image is to run::
     $ singularity build qsiprep-<version>.sif docker://pennbbl/qsiprep:<version>
 
 Where ``<version>`` should be replaced with the desired version of qsiprep that you want to download.
-Do not use ``latest``.
+Do not use ``latest`` or ``unstable`` unless you are performing limited testing.
 
 As with Docker, you will need to bind the Freesurfer license.txt when running Singularity ::
 
-    $ singularity run --cleanenv \
-        -B $HOME/fullds005:/data:ro,$HOME/dockerout:/out,${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
+    $ singularity run --containall --writable-tmpfs \
+        -B $HOME/fullds005,$HOME/dockerout,${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
         qsiprep-<version>.sif \
-        /data /out participant \
+        $HOME/fullds005 $HOME/dockerout participant \
         --fs-license-file /opt/freesurfer/license.txt
 
 
 External Dependencies
 ---------------------
 
-qsiprep is written using Python 3.6 (or above), and is based on
-nipype_.
-
-qsiprep requires some other non-python neuroimaging software tools:
-
-- ANTs_ (version 2.3.9)
-- AFNI_ (version Debian-16.2.07)
-- FreeSurfer_ (6.0.1)
-- FSL_ (6.0.3)
-- `DSI Studio`_
-- MRtrix_
+qsiprep is written using Python 3.8 (or above), and is based on
+nipype_. The external dependencies are built in the `qsiprep_build
+<https://github.com/PennLINC/qsiprep_build>`_ repository. There
+you can find the URLs used to download the dependency source code
+and the steps to compile each dependency.