From 7bc9e713c605cfbd09c13117a6f85be1b45b94c4 Mon Sep 17 00:00:00 2001 From: Leily Rabbani Date: Thu, 16 Jul 2020 16:05:39 +0200 Subject: [PATCH 1/2] updated conda installtion guideline --- docs/content/installation.rst | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/docs/content/installation.rst b/docs/content/installation.rst index 65cf21c7..121aeb80 100644 --- 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 +19,14 @@ 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 `_. -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 Command line installation using ``pip`` ----------------------------------------- @@ -49,7 +48,7 @@ If you need to specify a specific path for the installation of the tools, make u 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`. From a8eb216d10050f03077363c5b0500f8408424963 Mon Sep 17 00:00:00 2001 From: Leily Rabbani Date: Thu, 16 Jul 2020 16:40:44 +0200 Subject: [PATCH 2/2] more added to conda installation both on the installation.rst and README --- README.md | 11 ++++++++--- docs/content/installation.rst | 9 +++++++-- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index e7971810..ce954986 100644 --- 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). - External users diff --git a/docs/content/installation.rst b/docs/content/installation.rst index 121aeb80..5b632274 100644 --- a/docs/content/installation.rst +++ b/docs/content/installation.rst @@ -26,7 +26,13 @@ We encourage users to use ``conda`` installation to install pygenometracks. All .. code:: bash - $ conda create -n pygenometracks -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`` ----------------------------------------- @@ -44,7 +50,6 @@ 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`` -------------------------------------------