diff --git a/README.md b/README.md index 1d5563b3267d0efc7d3ae58533aaa8420a6f088e..34a4a05c3b9879852501b52b1c74d090b40c1c2c 100755 --- a/README.md +++ b/README.md @@ -98,6 +98,8 @@ You have different possibilities to install `PanACoTa`. ### <a name="pypi"></a> From pip +[](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 +[](http://bioconda.github.io/recipes/ppanggolin/README.html) + +[](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. diff --git a/doc/source/starting.rst b/doc/source/starting.rst index 7ca923a159248c4a9cd560a6e76c9da8b3ef0799..952883535ac063800bed4dc211c2d6af3364157c 100755 --- a/doc/source/starting.rst +++ b/doc/source/starting.rst @@ -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: