From 5616f7692d67f648b355149eb104cc204ec78b12 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Tue, 4 Jun 2024 10:25:00 -0500 Subject: [PATCH] Update PathLinker install instructions Delete pkg-resources line from requirements --- doc/pathlinker.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/doc/pathlinker.md b/doc/pathlinker.md index 7879097f..baf687a0 100644 --- a/doc/pathlinker.md +++ b/doc/pathlinker.md @@ -16,13 +16,13 @@ Start by reading this manuscript to gain a high-level understanding of its algor ## Step 2: Get the PathLinker files From the PathLinker GitHub repository , click Code and Download ZIP to download all the source and data files. -Unzip them on your local file system into a directory you’ll use for this project. +Unzip them on your local file system into a directory you’ll use for this project. ## Step 3: Install Anaconda (optional) If you do not already have Anaconda on your computer, install Anaconda so you can manage conda environments. -If you haven’t used conda before for Python, this [blog post](https://astrobiomike.github.io/unix/conda-intro) gives an overview of conda and why it is useful. -You don’t need most of the commands in it, but it can be a reference. +If you haven’t used conda before for Python, this [blog post](https://astrobiomike.github.io/unix/conda-intro) gives an overview of conda and why it is useful. +You don’t need most of the commands in it, but it can be a reference. You can download Anaconda from and follow the installation instructions. If you have the option to add Anaconda to your system `PATH` when installing it, which will make it your default version of Python, we recommend that. Anaconda will give you an initial default conda environment and some useful packages. @@ -32,7 +32,12 @@ A conda environment is an isolated collection of Python packages that enables yo Create a new conda environment for PathLinker called "pathlinker" with Python 3.5 and install the dependencies from a requirements file into that environment. PathLinker uses old versions of Python and dependencies like networkx, a package for working with graphs in Python. -From the project directory you created that contains the `requirements.txt` file from the PathLinker repository run: +The `requirements.txt` file contains an uninstallable package, so open it in a text editor and delete the line +``` +pkg-resources==0.0.0 +``` + +Then, from the project directory you created that contains the `requirements.txt` file from the PathLinker repository run: ``` conda create -n pathlinker python=3.5 conda activate pathlinker