From 934f5bdf7902e0d41135ae31e611d8989912c445 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Fri, 6 Nov 2020 10:24:48 +0100 Subject: [PATCH] Add conda installation --- README.md | 14 ++++++++++++++ doc/source/starting.rst | 18 ++++++++++++++++++ 2 files changed, 32 insertions(+) diff --git a/README.md b/README.md index 9afd2f2f..1d5563b3 100755 --- a/README.md +++ b/README.md @@ -51,6 +51,7 @@ Installation - [pip](#pypi) - [cloning github repository](#clone) - [singularity](#singularity) +- [conda](#conda) Running - [Quick run](#run) @@ -145,6 +146,19 @@ To get latest version: It will replace your file panacota.img by a new one corresponding to the latest version. +### <a name="conda"></a> 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: + + # 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 + conda activate myenv + # Install PanACoTA + conda install -c bioconda panacota + # When you have finished using PanACoTA, deactivate environment + conda deactivate + ### From zip version For people wanting to download source code of a specific version, we provide releases. You can download last one here: [](https://github.com/gem-pasteur/PanACoTA/releases) diff --git a/doc/source/starting.rst b/doc/source/starting.rst index cc4dc5dc..7ca923a1 100755 --- a/doc/source/starting.rst +++ b/doc/source/starting.rst @@ -134,6 +134,24 @@ To get latest version: It will replace your file ``panacota.img`` by a new one corresponding to the latest version. +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 + + 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 + conda activate myenv + # Install PanACoTA + conda install -c bioconda panacota + # When you have finished using PanACoTA, deactivate environment + conda deactivate + + From zip version **************** -- GitLab