Updating Readme and installation

README.rst

@@ -55,20 +55,17 @@ The installation can be performed directly from Pypi:
     # install R packages for circtools
     circtools_install_R_dependencies
 
-
-
 Additionally, this repository offers the latest development version:
 
 .. code-block:: console
 
     pip install numpy # required for HTSeq, a dependency of circtools
     pip install git+https://github.com/jakobilab/circtools.git
 
-
 The primer-design module as well as the exon analysis and circRNA testing module
 require a working installation of `R <https://cran.r-project.org/>`__ with
 `BioConductor <https://www.bioconductor.org/install/>`__. All R packages
-required are automatically installed during the setup. Please see the
+required can be automatically installed during the setup. Please see the
 `"Installing circtools" <http://docs.circ.tools/en/latest/Installation.html>`__
 chapter of the main circtools documentation for more detailed installation instructions.
 

docs/Installation.rst

@@ -19,13 +19,65 @@ The default installation will install everything needed to run circtools *except
 
 .. code-block:: bash
 
-    pip3 install circtools --user
+    python3 -m pip install circtools --user # will install only for the current user
 
 Please note:
 
 * The required R libraries will be installed in the default location in your home directory - unless you set enviromnet variable $R_LIBS_USER.
 * In case want to install globally or into a dedicated 'venv' drop the --user option.
 
+
+
+Installation via GitHub
+--------------------------
+
+The GitHub installation will install the most recent version directly from the source repository. Use this method if you want the latest fixes and features.
+
+.. code-block:: bash
+
+    git clone https://github.com/jakobilab/circtools.git
+    cd circtools
+    python3 -m pip install . --user
+
+
+Installation of R dependencies
+--------------------------------
+
+All R packages required by circtools can be automatically installed with a single command:
+
+.. code-block:: bash
+
+    circtools_install_R_dependencies
+
+The R packages require certain development libraries installed in order to be compiled from source.
+
+The following libraries are required (Ubuntu/Debian package names given):
+
+- libpng-dev
+- zlib1g-dev
+- libbz2-dev
+- libjpeg-turbo8-dev
+- libcurl4-openssl-dev
+- libxml2-dev
+- libblas-dev
+- liblzma-dev
+- libfontconfig1-dev
+- liblapack-dev
+- libssl-dev
+- libharfbuzz-dev
+- libfribidi-dev
+- libfreetype6-dev
+- libtiff5-dev
+- libjpeg-dev
+
+A simple command to install all of these libraries on an Ubuntu/Debian system would be:
+
+.. code-block:: bash
+
+    apt-get install --no-install-recommends r-base python3 python3-dev make g++ gfortran libpng-dev zlib1g-dev libbz2-dev libjpeg-turbo8-dev libcurl4-openssl-dev libxml2-dev libblas-dev liblzma-dev libfontconfig1-dev liblapack-dev libssl-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libtiff5-dev libjpeg-dev
+
+The command above only installs the minimal required packages, no other recommend packages are installed to keep the system lean.
+
 Installation via docker
 -----------------------------------
 
@@ -43,18 +95,6 @@ Subsequently, **circtools** can be run via
 
 Other than the additional command `docker run circtools` vs. just `circtools` all commands remain unchanged.
 
-
-Installation via GitHub
---------------------------
-
-The GitHub installation will install the most recent version directly from the source repository. Use this method if you want the latest fixes and features.
-
-.. code-block:: bash
-
-    git clone https://github.com/jakobilab/circtools.git
-    cd circtools
-    pip3 install . --verbose --user
-
 Updating circtools
 --------------------------
 
@@ -71,6 +111,19 @@ You may want to update the circtools package if new versions are published. Simi
     cd circtools/
     pip3 install . install --verbose --user --upgrade
 
+
+Finishing up
+------------------
+In order for circtools to find all executables, the setup will add the folder ``/home/$USER/.local/bin/`` automatically to your ``.bashrc`` file
+
+This closes the circtools installation. To verify that circtools has been correctly installed, try to call circtools for the first time:
+
+.. code-block:: bash
+
+    $> circtools --help
+    usage: circtools [-V] <command> [<args>]
+
+
 Required dependencies
 ---------------------
 
@@ -79,7 +132,7 @@ External tools
 
 * `bedtools [>= 2.27.1] <http://bedtools.readthedocs.io/en/latest/content/installation.html>`_ required by the enrichment module
 
-* `R [>= 4.0.0] <https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-16-04-2>`_ required by visualisation scripts and the primer design module
+* `R [>= 4.0.0] <https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-20.04>`_ required by visualisation scripts and the primer design module
 
 * `STAR [>= 2.6.0] <https://github.com/alexdobin/STAR>`_ required by the ``detect`` and ``reconstruct`` module to map RNA-seq reads against a reference genome and detect back splice junctions
 
@@ -100,43 +153,3 @@ Required Python packages (automatically installed)
 - reportlab >= 3.3.0
 - pandas >= 0.25.0
 - statsmodels >= 0.9.0
-
-Detailed manual installation
-----------------------
-
-Getting the source code
-^^^^^^^^^^^^^^^^^^^^^^^
-
-**Step 1**: Clone source code from GitHub:
-
-.. code-block:: bash
-
-    git clone https://github.com/jakobilab/circtools.git
-
-Installation
-^^^^^^^^^^^^
-
-**Step 2**: Install circtools using the provided installation script. The ``--user`` flag installs circtools in your home folder, thus making sure you do not require any administrative rights during the installation:
-
-.. code-block:: bash
-
-    cd circtools
-    pip3 install . install --verbose --user
-
-R environment
-^^^^^^^^^^^^^^
-
-**Step 3**: Setting up R environment. In order for the automatic installation of R packages to work we need to set the package directory to a user-writeable path. The setup automatically sets that path to ``/home/$USER/.R/``.
-
-
-Finishing up
-^^^^^^^^^^^^
-
-**Step 5**: Adding installation folder to ``$PATH``. In order for circtools to find all executables, the setup will add the folder ``/home/$USER/.local/bin/`` automatically to your ``.bashrc`` file
-
-This closes the circtools installation. To verify that circtools has been correctly installed, try to call circtools for the first time:
-
-.. code-block:: bash
-
-    $> circtools --help
-    usage: circtools [-V] <command> [<args>]