From 65f87d8c898e48406164574af9b5a737c1148544 Mon Sep 17 00:00:00 2001
From: Alex Kotlar <akotlar@bu.edu>
Date: Thu, 7 Sep 2023 11:36:00 -0400
Subject: [PATCH] Improve INSTALL.md; remove apt update from install-apt.sh

---
 INSTALL.md                  | 53 ++++++++++++++++++++++++++-----------
 install/install-apt-deps.sh |  3 +--
 2 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index b4d08280a..359040fb9 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -1,10 +1,8 @@
-# Bystro installation
-
 For most users, we recommend not installing the software, and using https://bystro.io, where the software is hosted
 
-The web app provides full functionality for any size experiment (up to 890GB uncompressed/129GB compressed tested), a convenient search interface, and excellent performance
+The web app provides full functionality for any size experiment, a convenient search interface, and excellent performance
 
-## Docker
+# Installing Bystro using Docker
 
 ###### The recommended way to use Bystro on the command line
 
@@ -19,29 +17,54 @@ docker run bystro bystro-annotate.pl #Annotate
 docker run bystro bystro-build.pl #Build
 ```
 
-## Installation on RPM-based distros
+# Direct (non-Docker) installation
 
-###### (Fedora, Redhat, Centos, openSUSE, Mandriva)
+There are 2 components to Bystro:
+ 1. The Bystro annotator: a Perl program accessed through the command line (via bin/bystro-*)
+ 2. The Bystro Python package: where the rest of Bystro's functionality lives (statistics, proteomics, etc).
 
-1.  `git clone https://github.com/akotlar/bystro.git && cd bystro && source ./install-rpm.sh`
+## Installing the Bystro annotator (Perl/cli)
+
+##### (Fedora, Redhat, Centos, openSUSE, Mandriva)
 
-## Installation on MacOS
+1.  `git clone https://github.com/akotlar/bystro.git && cd bystro && source ./install-rpm.sh`
 
-###### (tested on HighSierra, interactive)
+##### MacOS (tested on HighSierra, interactive)
 
 1.  `git clone https://github.com/akotlar/bystro.git && cd bystro && source ./install-mac.sh`
 
-## Installation on Debian systems
+##### Ubuntu
+1.  Ensure that packages are up to date (`sudo apt update`), or that you are satisified with the state of package versions.
+2.  `git clone https://github.com/akotlar/bystro.git && cd bystro && source ./install-apt.sh`
+    - Please note that this installation script requires root priveleges, in order to install system dependencies
+
+## Installing the Bystro Python libraries and cli tools
+
+We recommend using Miniconda to manage Bystro Python dependencies: https://docs.conda.io/projects/miniconda/en/latest/
 
-###### (Ubuntu)
+Once Bystro annotator installation is complete, and assuming Conda/Miniconda has been installed, run :
 
-1.  `git clone https://github.com/akotlar/bystro.git && cd bystro && source ./install-apt.sh`
+```sh
+# Install Rust
+curl https://sh.rustup.rs -sSf | sh -s -- -y
+echo -e "\n### Bystro: Done installing Rust! Now sourcing .cargo/env for use in the current shell ###\n"
+source "$HOME/.cargo/env"
+# Create or activate Bystro conda environment and install all dependencies
+# This assumes you are in the bystro folder
+source .initialize_conda_env.sh;
+```
+
+to install the Python package dependencies. Then, run:
+```
+# Build the Python package for local use
+make build
+```
 
-## Example of installation on RPM-based Amazon AMI (any 'yum'-capable Amazon AMI)
+to intall the Bystro Python library.
 
-Run the script found @ https://github.com/akotlar/bystro-aws
+Follow the instructions below to install the Bystro annotator:
 
-## Configuring Bystro for annotation
+## Configuring the Bystro annotator
 
 Once Bystro is installed, it needs to be configured. The easiest step is choosing the species/assemblies to annotate.
 
diff --git a/install/install-apt-deps.sh b/install/install-apt-deps.sh
index 5296a56c2..70b526921 100755
--- a/install/install-apt-deps.sh
+++ b/install/install-apt-deps.sh
@@ -2,7 +2,6 @@
 
 echo -e "\n\nInstalling Ubuntu/Debian (apt-get) dependencies\n";
 
-sudo apt update;
 # Installs gcc, and more; may be too much
 sudo apt install -y build-essential;
 
@@ -31,4 +30,4 @@ sudo apt install -y nodejs;
 sudo apt install -y npm;
 sudo npm install -g pm2;
 
-sudo apt install -y awscli;
\ No newline at end of file
+sudo apt install -y awscli;