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Commit 5c57768c authored by Amandine  PERRIN's avatar Amandine PERRIN
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Complete installation instructions

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......@@ -98,6 +98,8 @@ You have different possibilities to install `PanACoTa`.
### <a name="pypi"></a> From pip
[![PyPI version](https://badge.fury.io/py/PanACoTA.svg)](https://badge.fury.io/py/PanACoTA)
A very simple way to install the last stable version. This will install files in your python site-packages folder.
pip install panacota
......@@ -148,6 +150,10 @@ It will replace your file panacota.img by a new one corresponding to the latest
### <a name="conda"></a> From conda
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/ppanggolin/README.html)
[![Anaconda-Server Badge](https://anaconda.org/bioconda/panacota/badges/version.svg)](https://anaconda.org/bioconda/panacota)
Be careful while using conda, especially if you are not familiar with it. We advise to install PanACoTA in a dedicated conda environment, in order to avoid unwanted interactions with other softwares (like needed versions of dependencies automatically installed by conda). To install the package, use `conda install -c bioconda panacota`. But, as described in [conda documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#id6), we advise to install it with:
# Create an environment: This creates the 'myenv' environment in '/envs/'. No packages will be installed in this environment.
......
......@@ -104,15 +104,10 @@ To upload to new version, go back to your repository:
git pull
./make upgrade
From singularity image
**********************
.. _singularity:
|singularity|
.. |singularity| image:: https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg
:target: https://singularity-hub.org/collections/4724
From singularity image
**********************
Very useful if you do not have permission rights on the computer, such as, for example, on a cluster. The other advantage is that you do not need to install any dependence (except singularity itself of course). Singularity image includes all of them. You just have to download 1 file, and nothing will be installed anywhere on your computer.
......@@ -139,9 +134,8 @@ From conda
Be careful while using conda, especially if you are not familiar with it. We advise to install PanACoTA in a dedicated conda environment, in order to avoid unwanted interactions with other softwares (like needed versions of dependencies automatically installed by conda). To install the package, use ``conda install -c bioconda panacota``. But, as described in `conda documentation <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#id6>`_, we advise to install it with:
.... code-block:: bash
.. code-block:: bash
source
# Create an environment: This creates the 'myenv' environment in '/envs/'. No packages will be installed in this environment.
conda create --name myenv
# Activate the environment
......@@ -156,13 +150,13 @@ Be careful while using conda, especially if you are not familiar with it. We adv
From zip version
****************
For people wanting to download source code of a specific version, we provide releases. You can download last one here:
|zip|
.. |zip| image:: https://img.shields.io/github/release/gem-pasteur/PanACoTA.svg
:target: https://github.com/gem-pasteur/PanACoTA/releases
For people wanting to download source code of a specific version, we provide releases. You can download last one here:
.. _installing:
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