From a4fe325dc8c7c3cc2263b5d5d31e672ca977e073 Mon Sep 17 00:00:00 2001 From: vbhardwaj Date: Thu, 25 Jul 2024 12:11:14 +0200 Subject: [PATCH] updated install instructions --- README.md | 14 +++++++------- docs/index.rst | 46 ++++++++++++++++++++++++++++++++++++++-------- 2 files changed, 45 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index b678299..e82f5a5 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ## sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data. -[![DOI](https://zenodo.org/badge/271841139.svg)](https://zenodo.org/badge/latestdoi/271841139) [![Documentation Status](https://readthedocs.org/projects/sincei/badge/?version=latest)](https://sincei.readthedocs.io/en/latest/?badge=latest) [![PyPI Version](https://img.shields.io/pypi/v/sincei.svg?style=plastic)](https://pypi.org/project/sincei/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![test](https://github.com/vivekbhr/sincei/actions/workflows/test.yml/badge.svg)](https://github.com/vivekbhr/sincei/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/vivekbhr/sincei/graph/badge.svg?token=VRTMITHHBI)](https://codecov.io/gh/vivekbhr/sincei) +[![DOI](https://zenodo.org/badge/271841139.svg)](https://zenodo.org/badge/latestdoi/271841139) [![Documentation Status](https://readthedocs.org/projects/sincei/badge/?version=latest)](https://sincei.readthedocs.io/en/latest/?badge=latest) [![PyPI Version](https://img.shields.io/pypi/v/sincei.svg?style=plastic)](https://pypi.org/project/sincei/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![test](https://github.com/vivekbhr/sincei/actions/workflows/test.yml/badge.svg)](https://github.com/vivekbhr/sincei/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/vivekbhr/sincei/graph/badge.svg?token=VRTMITHHBI)](https://codecov.io/gh/vivekbhr/sincei) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sincei/README.html) ## Features @@ -23,18 +23,18 @@ Please browse the full documentation for tutorials on how to use sincei on comma sincei is a command line toolkit based on python3, and can be installed using [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html). -Create a new conda environment and install sincei stable release from github using: +The recommended way to install sincei is via bioconda: ``` -conda create -n sincei -c anaconda python=3.8 -conda activate sincei -(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@master#egg=sincei +conda create -n sincei -c bioconda -c conda-forge sincei ``` -For the development version, try: +Alternatively, a development version can be installed via GitHub. ``` -(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@develop#egg=sincei +conda create -n sincei -c anaconda python=3.8 +conda activate sincei +(sincei): pip install --editable=git+https://github.com/bhardwaj-lab/sincei.git@master#egg=sincei ``` ## Usage diff --git a/docs/index.rst b/docs/index.rst index 63b4910..dbcec74 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -16,31 +16,61 @@ :target: https://pypi.org/project/sincei/ :alt: PyPI Version +.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat + :target: http://bioconda.github.io/recipes/sincei/README.html + :alt: Install with bioconda + Bhardwaj V. and Mourragui S. (2023) sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data. +================= +Installation +================= +sincei is a command line toolkit based on python3. The stable version of sincei can be installed using `conda `_ , while the development versions can be installed from github via pip. -Installation -------------------- -sincei is a command line toolkit based on python3, and can be installed using `conda `_ +Installation via bioconda +--------------------------- + +Create a new conda environment and install sincei in it using: + +.. code-block:: bash + + conda create -n sincei -c bioconda -c conda-forge sincei + +Users of Mac with Arm architecture (M1-3 macbooks and beyond) should explicitly specify the osx-64 version to allow dependencies to install properly. + +.. code-block:: bash + + conda create -n sincei --subdir 'osx-64' -c bioconda -c conda-forge sincei -Create a new conda environment and install sincei using: +*Note:* The dependency `mctorch-lib` required for `scClusterCells` is currently unavailable via conda, therefore, to use `scClusterCells`, we recommend installing it separately via pip. + +.. code-block:: bash + + # install mctorch-lib + (sincei): pip install mctorch-lib + (sincei): scClusterCells --help + + +Installation via github +--------------------------- + +Create a new conda environment and install sincei in it using pip from GitHub: .. code-block:: bash conda create -n sincei -c anaconda python=3.8 conda activate sincei - (sincei): pip install git+https://github.com/vivekbhr/sincei.git@master#egg=sincei + (sincei): pip install git+https://github.com/bhardwaj-lab/sincei.git@master#egg=sincei Getting Help ------------ -* For all kind of questions, suggesting changes/enhancements or to report bugs, please create an issue on `our GitHub repository `_ - -**Please Note that sincei is under active development.** Some features might be incomplete, untested or might be removed as we move towards a stable version. +* For questions related to usage, or suggesting changes/enhancements please use our `GitHub discussion board `__ . To report bugs, please create an issue on `our GitHub repository `_ +**Please Note that sincei is under active development.** We expect significant changes/updates as we move towards our first major release (1.0). The list of tools available in sincei