From 581141857ec94df48573872810023692f3ddf394 Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Sun, 8 Dec 2024 07:37:02 +0100 Subject: [PATCH] expanded install docs for orthohmm --- docs/index.rst | 28 +++++++++++++++++++++++----- 1 file changed, 23 insertions(+), 5 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 3fe7503..1c95f86 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,7 +17,14 @@ If you found OrthoHMM useful, please cite *MANUSCRIPT TITLE*. Steenwyk et al. 20 Quick Start ----------- -These two lines represent the simpliest method to rapidly install and run OrthoHMM. +1\. Install external dependencies + +OrthoHMM has two external dependencies — [HMMER](http://hmmer.org/download.html) and [mcl](https://github.com/micans/mcl?tab=readme-ov-file#installation-and-mcl-versions) — that can't be installed using pip. +Download and install these programs from their respective websites, which are linked in the previous sentence. + +| + +2\. Install OrthoHMM .. code-block:: shell @@ -32,11 +39,16 @@ Below are more detailed instructions, including alternative installation methods **1) Installation** -To help ensure OrthoHMM can be installed using your favorite workflow, we have made OrthoHMM available from pip, source, and the anaconda cloud. +**If you are having trouble installing OrthoHMM, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [Bluesky](https://bsky.app/profile/jlsteenwyk.bsky.social) to get help.** + +1\. Install external dependencies + +OrthoHMM has two external dependencies — [HMMER](http://hmmer.org/download.html) and [mcl](https://github.com/micans/mcl?tab=readme-ov-file#installation-and-mcl-versions) — that can't be installed using pip. +Download and install these programs from their respective websites, which are linked in the previous sentence. -**Install from pip** +2a\. Install OrthoHMM from pip -To install from pip, use the following commands: +To install using *pip*, we recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands: .. code-block:: shell @@ -74,7 +86,13 @@ To deactivate your virtual environment, use the following command: # deactivate virtual environment deactivate -**Note, the virtual environment must be activated to use orthohmm.** +Note, the virtual environment must be activated to use orthohmm. + +| + +2b\. Install OrthoHMM from source + +Similarly, to install from source, we recommend using a virtual environment. To do so, use the following commands: .. code-block:: shell