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updated conda installtion guideline #268

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Jul 16, 2020
Merged

updated conda installtion guideline #268

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7bc9e71
updated conda installtion guideline
Jul 16, 2020
a8eb216
more added to conda installation both on the installation.rst and README
Jul 16, 2020
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11 changes: 8 additions & 3 deletions README.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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22 changes: 13 additions & 9 deletions docs/content/installation.rst
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Expand Up @@ -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
Expand All @@ -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``
-----------------------------------------
Expand All @@ -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`.

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