Merge pull request #422 from maxplanck-ie/docs_vivek

Doc update about the conda issue

README.rst

@@ -17,6 +17,12 @@ snakePipes
 
 snakePipes are flexible and powerful workflows built using `snakemake <snakemake.readthedocs.io>`__ that simplify the analysis of NGS data.
 
+.. image:: ./docs/content/images/snakePipes.png
+   :scale: 20 %
+   :height: 100px
+   :width: 100 px
+   :align: right
+
 Workflows available
 --------------------
 
@@ -41,7 +47,7 @@ Afterward, simply run the following:
 
 This will create a new conda environment called "snakePipes" into which snakePipes is installed. You will then need to create the conda environments needed by the various workflows. To facilitate this we provide the `snakePipes` commands:
 
-* ``source activate snakePipes`` to activate the appropriate conda environment.
+* ``conda activate snakePipes`` to activate the appropriate conda environment.
 * ``snakePipes createEnvs`` to create the various environments and register GATK.
 
 Indices and annotations needed to run the workflows could be created by a simple command :

docs/content/advanced_usage.rst

@@ -204,7 +204,7 @@ Below is an example of running the RNA-seq pipeline on AWS using the resources o
     conda config --set always_yes yes --set changeps1 no
     conda update -q conda
     conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes
-    source activate snakePipes
+    conda activate snakePipes
     rm Miniconda3-latest-Linux-x86_64.sh
 
     # setup snakePipes
@@ -220,7 +220,7 @@ Then a larger instance can be spun up and the `RNA-seq` pipeline run as normal.
     mount /dev/sdf1 /data
     chown ec2-user /data
     export PATH=/data/snakePipes/bin:$PATH
-    source activate snakePipes
+    conda activate snakePipes
     RNA-seq -m alignment -i /data/data -o /data/output --local -j 192 /data/indices/GRCm28.yaml
 
 Receiving emails upon pipeline completion

docs/content/setting_up.rst

@@ -8,7 +8,7 @@ Unlike many other pipelines, setting up snakePipes is easy! All you need is a *l
 Installing conda with python3
 -----------------------------
 
-Follow the instructions `here <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`__ to install either
+Follow the instructions `here <https://conda.io/docs/user-guide/install/index.html>`__ to install either
 miniconda or anaconda. A minimal version (miniconda) is enough for snakePipes. Get the miniconda installer `here <https://conda.io/miniconda.html>`__.
 
 After installation, check your python path and version :
@@ -53,32 +53,28 @@ Instead of providing the URL to ``pip``, you can also `clone <https://help.githu
 
 .. note:: Using the --user argument would install the program into ``~/.local/bin/``. So make sure to have it in your $PATH before executing any workflow.
 
-Next, activate snakePipes.
 
+Testing whether the installation went fine
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+After installation, you can activate the snakePipes environment via
 
-Activate snakePipes
----------------------
 .. code:: bash
 
     conda activate snakePipes
 
-    
-Snakemake and pandas are installed as requirements. Ensure you have everything working by testing these commands:
-
-.. code-block:: bash
-
-    snakemake --help
-    snakePipes --help
+In case you installed conda using the latest version of conda installers (eg. minicoda `4.5.*` or later), the `conda` command might not be available inside an environment. To enable this, export the path to conda/bin in your $PATH (or append the path manually in your `bashrc`)
 
+.. code:: bash
 
-Remove example organism YAML files
-----------------------------------
+    export PATH="/path/to/miniconda3/bin:$PATH"
 
-There are a number of example organism YAML files (see the next section). You will likely want to remove these as follows:
+Snakemake and pandas are installed along with snakePipes as requirements. Ensure you have them working by testing these commands:
 
-.. code:: bash
+.. code-block:: bash
 
-    snakePipes flushOrganisms
+    snakemake --help
+    snakePipes --help
 
 
 Inspect and modify the setup files

docs/index.rst

@@ -1,8 +1,14 @@
 snakePipes
 ==========
 
+.. image:: content/images/snakePipes.png
+   :scale: 20 %
+   :height: 200px
+   :width: 200 px
+
 snakePipes are pipelines built using `snakemake <snakemake.readthedocs.io>`__ and *python* for the analysis of epigenomic datasets.
 
+
 Below is the list of pipelines available in snakePipes
 ------------------------------------------------------