diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index fd3d775e7d4322e6df69b7858fb9aa8af98da7e5..2a1a2743e15173aad3d94ea4517c91be651c92a7 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,7 +1,7 @@
Changes in Release <RELEASE NUMBER>
--------------------------------------------------------------------------------
- * Introduced recipes to generate Docker and Singularity containers.
+ * Introduced recipes to generate Docker and Singularity images.
* Moved "nonstandard" functions from ost.conop to ost.mol.alg. Mapping
functions CopyResidue, CopyConserved and CopyNonConserved that were
previousely imported from ost.conop are now to be imported from ost.mol.alg.
diff --git a/docker/README.rst b/docker/README.rst
index 4700eb156cad0663893a957ff0eb42aafbffac7e..ebed4e994c2aac8045b0f1171fb38948bb19d849 100644
--- a/docker/README.rst
+++ b/docker/README.rst
@@ -4,7 +4,7 @@ OST Docker
.. note::
For many docker installations it is required to run docker commands as root. As
- this depends on set up, we skip the `sudo` in all commands.
+ this depends on set up, we skip the ``sudo`` in all commands.
Build Docker image
------------------
@@ -23,15 +23,19 @@ or if you downloaded the Dockerfile directly:
docker build --tag <IMAGE NAME> --build-arg OPENSTRUCTURE_VERSION=<VERSION> -f <DOCKERFILE NAME> <PATH TO DOCKERFILE DIR>
-You can chose any image name (tag) eg. ost. The `OPENSTRUCTURE_VERSION`
+You can chose any image name (tag) eg. ost. The ``OPENSTRUCTURE_VERSION``
build argument is mandatory and image will not built without it. See
`CHANGELOG <https://git.scicore.unibas.ch/schwede/openstructure/blob/master/CHANGELOG.txt>`_
-for current list of available releases.
+for current list of available releases. This is not expected to work for
+versions which are much older than the most recent one since the dependencies
+might have changed, but it should work for a few versions. If you need the
+recipe for an older version, we suggest to get an older recipe from the git
+history.
Testing the image
-----------------
-One can find a exemplary script (`test_docker.py`) in the downloaded directory.
+One can find a exemplary script (``test_docker.py``) in the downloaded directory.
To run it do:
.. code-block::
@@ -39,7 +43,7 @@ To run it do:
cd <PATH TO OST>/docker
docker run --rm -v $(pwd):/home <IMAGE NAME> test_docker.py
-As the last line you should see `OST is working!`.
+As the last line you should see ``OST is working!``.
Run script and action with OST
------------------------------
@@ -61,7 +65,7 @@ Run script and action with OST
.. code-block:: bash
- docker run --rm -v /home/user:/home <IMAGE NAME> home/script.py /home/pdbs/struct.pdb
+ docker run --rm -v /home/user:/home <IMAGE NAME> /home/script.py /home/pdbs/struct.pdb
An easy solution to mount a CWD is to use $(pwd) command in the -v option
of the Docker. For an example see the action exemplary run.
@@ -83,7 +87,7 @@ To run chosen action do:
docker run --rm <IMAGE NAME> <ACTION NAME>
-Here is an example run of compare-structures action mimicking CAMEO evaluation:
+Here is an example run of the compare-structures action:
.. code-block::
@@ -123,7 +127,7 @@ In order to run OST script do:
Run ost with utility command
###############################
-One can also use provided utility bash script `run_docker_ost` to run basic
+One can also use provided utility bash script ``run_docker_ost`` to run basic
scripts and actions:
.. code-block:: bash
@@ -137,7 +141,7 @@ options. It is useful to link the command to the binary directory eg. in linux:
ln -s <PATH TO OST>/docker/run_docker_ost /usr/bin/run_docker_ost
-In order to run an exemplary script (`test_docker.py`) do:
+In order to run an exemplary script (``test_docker.py``) do:
.. code-block::
@@ -170,13 +174,13 @@ the entrypoint:
.. code-block::
- sudo docker run --rm -ti --entrypoint <COMMAND> <IMAGE NAME> [COMMAND OPTIONS]
+ docker run --rm -ti --entrypoint <COMMAND> <IMAGE NAME> [COMMAND OPTIONS]
Eg. to run molck type:
.. code-block::
- sudo docker run --rm -ti --entrypoint molck <IMAGE NAME> --help
+ docker run --rm -ti --entrypoint molck <IMAGE NAME> --help
.. note::
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 36e74440821905a303fd7a501268cfc422c17767..b6664cfb40580cca4d28a2271ac3cd34af8c05d7 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -4,14 +4,22 @@ Installing OpenStructure From Source
Brief Overview
--------------------------------------------------------------------------------
-Compiling OpenStructure consists of several steps that are described below in
-more detail. In essence, these steps are:
+For a simple and portable way to use OpenStructure we recommend using a
+container solution. We provide recipes to build images for
+`Docker <https://www.docker.com/>`_ and
+`Singularity <https://www.sylabs.io/guides/2.5.1/user-guide>`_.
+The latest recipes and instructions can be found on our GitLab site
+(`Docker instructions <https://git.scicore.unibas.ch/schwede/openstructure/tree/develop/docker>`_ and
+`Singularity instructions <https://git.scicore.unibas.ch/schwede/openstructure/tree/develop/singularity>`_).
+
+If you wish to compile OpenStructure outside of a container, you need to follow
+the steps which we describe in detail below. In essence, these steps are:
* Installing the Dependencies
* Checking out the source code from GIT
* Configuring the build with cmake
* Compiling an Linking
-
+
Installing the Dependencies
--------------------------------------------------------------------------------
diff --git a/singularity/README.rst b/singularity/README.rst
index f3e57b7760263c762341e99cf562e21593bf132f..fe7bb623c1a915694bc71e6c75e946f36da93b72 100644
--- a/singularity/README.rst
+++ b/singularity/README.rst
@@ -16,7 +16,12 @@ In order to build OST Singularity image:
Running singularity build command requires root permissions (sudo).
One can chose any name for an image. For the purose of this file we will assume
-that the image name is `ost.img`.
+that the image name is ``ost.img``.
+
+Here we only keep the recipe for the most recent version of OpenStructure. To
+build an image for a different version, you can either adapt the
+``OPENSTRUCTURE_VERSION`` variable in the recipe or look in the git history for
+an older recipe.
Available apps
--------------
@@ -58,5 +63,5 @@ Then (in the same terminal window) to invoke IPython app one can just type:
ost_ipython
-To make the alias permanent put it into your `.bashrc` file or whatever file you
-use to store the aliases.
\ No newline at end of file
+To make the alias permanent put it into your ``.bashrc`` file or whatever file
+you use to store the aliases.