Version 1.6, see Changelog for details

VERSION

-1.5.1
+1.6

docs/chapter1.rst

@@ -9,7 +9,7 @@ Principally, there are two ways of installing *diffTF* and the proper tools:
 
 1a. **The "easy" way**: Using ``Singularity`` and our preconfigured *diffTF* containers that contain all necessary tools, R, and R libraries
 
-  You only need to install Snakemake (see below for details) and ``Singularity``. Snakemake supports Singularity in Versions >=2.4. You can check whether you already have ``Singularity`` installed by simply typing
+  You only need to install Snakemake (see below for details) and ``Singularity``. *Snakemake* supports Singularity in Versions >=2.4. You can check whether you already have ``Singularity`` installed by simply typing
 
   .. code-block:: Bash
 
@@ -161,10 +161,12 @@ Adaptations and notes when running with Singularity
 ============================================================
  With ``Singularity``, each rule will be executed in pre-configured isolated containers that contain all necessary tools.  To enable it, you only have to add the following arguments when you execute Snakemake:
 
-1. ``--use-singularity``: Just type it like this, that's all!
+1. ``--use-singularity``: Just type it like this!
 
 2. ``--singularity-args``: You need to make all directories that contain files that are referenced in the *diffTF* configuration file available within the container also. By default, only the directory and subdirectories from which you start the analysis are automatically mounted inside the container. Since the *diffTF* source code is outside the ``input`` folder for the example analysis, however, at least the root directory of the Git repository has to be mounted. This is actually quite simple! Just use ``--singularity-args "--bind /your/diffTF/path"`` and replace ``/your/diffTF/path`` with the root path in which you cloned the *diffTF* Git repository (the one that has the subfolders ``example``, ``src`` etc.). If you reference additional files, simply add one or multiple directories to the bind path (use the comma to separate them). For example, if you reference the files ``/g/group1/user1/mm10.fa`` and ``/g/group2/user1/files/bla.txt`` in the configuration file file, you may add ``/g/group1/user1,/g/group2/user1/files`` or even just ``/g`` to the bind path (as all files you reference are within ``/g``).
 
+  .. note:: We note again that within a Singularity container, you cannot access paths outside of the directory from where you started executing Snakemake. If you receive errors in the ``checkParameterValidity`` rule that a directory does not exist even though you can cd into it, you most likely forgot to include the path this folder or a parent path as part of the ``bind`` option.
+
 3. ``--singularity-prefix /your/directory`` (optional): You do not have to, but you may want to add the ``--singularity-prefix`` argument to store all ``Singularity`` containers in a central place (here: ``/your/directory``) instead of the local ``.snakemake`` directory. If you intend to run multiple *diffTF* analyses in different folders, you can save space and time because the containers won't have to be downloaded each time and stored in multiple locations.
 
 Please read the following additional notes and warnings related to ``Singularity``:

docs/conf.py

@@ -47,7 +47,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'diffTF'
-copyright = '2019, Christian Arnold, Ivan Berest, Judith B. Zaugg'
+copyright = '2020, Christian Arnold, Ivan Berest, Judith B. Zaugg'
 author = 'Christian Arnold, Ivan Berest, Judith B. Zaugg'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -55,9 +55,9 @@ author = 'Christian Arnold, Ivan Berest, Judith B. Zaugg'
 # built documents.
 #
 # The short X.Y version.
-version = '1.5'
+version = '1.6'
 # The full version, including alpha/beta/rc tags.
-release = '1.5'
+release = '1.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/projectInfo.rst

@@ -63,6 +63,9 @@ Open Access. DOI: `https://doi.org/10.1016/j.celrep.2019.10.106 <https://doi.org
 
 Change log
 ============================
+Version 1.6 (2020-01-22)
+  - The documentation received a major update, in particular the section output files. In addition, a few new methodological figures have been added as well as an interpretation section.
+
 Version 1.5 (2019-12-03)
   - *diffTF* has been published in Cell Reports! See the section :ref:`citation` for details.
   - raw and adjusted p-values for the permutation-based approach can now not be 0 anymore. We now use the approach described `here <https://genomicsclass.github.io/book/pages/permutation_tests.html>`_. In a nutshell, the smallest p-value is now 1/(*nPermutations* + 1), with *nPermutations* denoting the number of permutations and thereby depends on the number of permutations - having more permutations makes the minimum p-value smaller.