Merge pull request #268 from deeptools/doc_installation

updated conda installtion guideline
deeptools · Jul 16, 2020 · fb7633e · fb7633e
2 parents 810fa31 + a8eb216
commit fb7633e
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diff --git a/README.md b/README.md
@@ -39,10 +39,15 @@ Installation
 ------------
 pyGenomeTracks works with python >=3.6.
 
-Currently, the best way to install pyGenomeTracks is with anaconda
+The recommended way to install pyGenomeTracks is via conda
 
 ```bash
-$ conda install -c bioconda -c conda-forge pygenometracks
+$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks pyhon=3.7
+```
+To get a specific version, one can specify it. For example:
+
+```bash
+$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 pyhon=3.7
 ```
 
 Also, pyGenomeTracks can be installed using pip
@@ -130,7 +135,7 @@ Documentation
 
 Our [documentation](http://pygenometracks.readthedocs.io/) provide [examples](http://pygenometracks.readthedocs.org/en/latest/content/examples.html), as well as the [full list of possible parameters](http://pygenometracks.readthedocs.org/en/latest/content/possible-parameters.html) and [guidelines for developers who would like to add a new track type](http://pygenometracks.readthedocs.org/en/latest/content/adding-new-tracks.html).
 
-<!-- I do not know what to do with that, is it External users? 
+<!-- I do not know what to do with that, is it External users?
 pyGenomeTracks is used by [HiCExporer](https://hicexplorer.readthedocs.io/) and [HiCBrowser](https://github.com/maxplanck-ie/HiCBrowser) (See e.g. [Chorogenome navigator](http://chorogenome.ie-freiburg.mpg.de/) which is made with HiCBrowser)
  -->
 External users

diff --git a/docs/content/installation.rst b/docs/content/installation.rst
@@ -4,7 +4,7 @@ Installation
 Remember -- pyGenomeTracks is available for **command line usage** as well as for
 **integration into Galaxy servers**!
 
-.. contents:: 
+.. contents::
     :local:
 
 Requirements
@@ -19,15 +19,20 @@ Requirements
 * matplotlib >= 3.1.1
 * gffutils >=0.9
 
-The fastest way to obtain **Python 3.6 together with numpy** is
-via the `Anaconda Scientific Python
-Distribution <https://store.continuum.io/cshop/anaconda/>`_.
-Just download the version that's suitable for your operating system and
-follow the directions for its installation. All of the requirements for pyGenomeTracks can be installed in Anaconda with:
+Command line installation using ``conda``
+-----------------------------------------
+
+We encourage users to use ``conda`` installation to install pygenometracks. All of the requirements for pyGenomeTracks can be installed via Anaconda with:
 
 .. code:: bash
 
-    $ conda install -c bioconda -c conda-forge pygenometracks
+    $ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks pyhon=3.7
+
+To get a specific version, one can specify it. For example:
+
+.. code:: bash
+
+    $ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 pyhon=3.7
 
 Command line installation using ``pip``
 -----------------------------------------
@@ -45,11 +50,10 @@ If you need to specify a specific path for the installation of the tools, make u
 
     $ pip install --install-option="--prefix=/MyPath/Tools/pyGenomeTracks" git+https://github.com/deeptools/pyGenomeTracks.git
 
-
 Command line installation without ``pip``
 -------------------------------------------
 
-You are highly recommended to use `pip` rather than these more complicated steps.
+You are highly recommended to use `conda install` rather than the following complicated steps.
 
 1. Install the requirements listed above in the "requirements" section. This is done automatically by `pip`.