View source for Installing Anaconda and the LabBorg Python Module

== Computer Systems Tested ==

* Windows 10 
*Mac OS Ventura 13.2 (Apple M1) 
**Should work for MaOS >= 11.0. 
**I am trying to get it to work on a MacOS 10.13, but that will take time. 

== Installation Procedure ==
# [https://www.anaconda.com/ Download and Install Anaconda]
##This takes a while about 10-15 minutes.
##Install Anaconda in your user directory and not as administrator.
##If you have a Mac with an ARM processor, click the apple and about. It will say either Apple M1 or M2. Use the '''X86_64.pkg''' at the end of the Anaconda installer (not the arm64.pkg). At the end, the installer will say that it failed but ignore that.
#Open Anaconda Navigator
##If it asks for you to update the program, click '''Yes'''. When prompted, click '''Update Now'''. When it is finished, click '''Launch Anaconda Navigator'''.
##If you did it correctly, it should look like: [[File:Ana23001.png|frameless]]
#On the left side, click [[File:Ana23002.png|frameless]]
##If you did it correctly, it should look like: [[File:Ana23003.png|frameless]]
#Click the [[File:Ana23004.png|frameless]]
#In the Create Environment Dialog, put some name like Jupyter37 and be sure that the Python version is 3.7. something.
##If you did it correctly, it should look like: [[File:Ana23005.png|frameless]]
#Click [[File:Ana23006.png|frameless]]
##This will take a while.
##When you are finished, it should look like this: [[File:Ana23007.png|frameless]]
#Download YYMMDD-Installer.zip from ELC New and put it somewhere where you can find it. The name might be something like 230123-Installer.zip.
##You should be able to repeat this procedure for any other versions.
#Unzip YYMMDD-Installer.zip. This will produce a folder called Installer.
#Put a folder called '''PHRM8010''' on your Desktop or some other location that you can find it.
#Navigate to the '''Installer''' that you unzipped. In Windows, an '''Installer''' directory might be in an '''Installer''' directory.
##Ultimately, you will get the following folder: [[File:Ana23008.png|frameless]]
#Navigate to the '''LabBorg''' folder, then '''Examples''', and copy the '''Jupyter''' Folder and put it into the '''PHRM8010''' directory that you created.
##These examples will be useful for you to try out different things in Python.
#If the '''Anaconda''' program is not already open, open it. Click environments on the left hand side.
#Select the environment that you created. In this example, it is Jupyter37.
#Click the [[File:Ana23009.png|frameless]] and select Open Terminal...
##If you did it correctly in Windows, it should look like: [[File:Ana23010.png|frameless]]
##It should look very similar on a Mac.
#Navigate to the Installer folder that you unzipped on the command line.
##For Windows, you will use two DOS commands: '''cd''' and '''dir''' for change directory and list directory, respectively.
##For Mac, you will use two Linux commands: '''cd''' and '''ls''' for change directory and list directory, respectively.
##For example, from the command prompt, I typed the following:
###cd Downloads
###dir
####Gives me the following output: [[File:Ana23011.png|frameless]]
####This command will be ls on the Mac.
###cd Installer
####Gives me the following output: [[File:Ana23012.png|frameless]]
####If you only see the directory Installer in Windows, type cd Installer again.
#Check to see if setup.py is in the directory list. If it is, type: '''python setup.py install'''
##If it is working, you should get the following output: [[File:Ana23013.png|frameless]]
##If this is the first time, installation might take about 30 minutes to complete.
#At the end, you should get the following dialog box: [[File:Ana23024.png|frameless]]
#Select the '''PHRM8010''' folder that you made.
#Exit and restart Anaconda Navigator.
#Select '''Environment''' on the left and the environment that you created. In my case, it was '''Jupyter37'''.
##If you did it correctly, you should see the following output: [[File:Ana23015.png|frameless]]
#Select '''Home'''
##If you did it correctly, you should see the following output:[[File:Ana23016.png|frameless]]
#[[File:Ana23017.png|frameless]]should be under the [[File:Ana23018.png|frameless]]Icon. If it is not, restart the Anaconda program.
#Click [[File:Ana23017.png|frameless]]
#JupyterLab should appear like the following in your browser: [[File:Ana23019.png|frameless]]

== Testing Procedure ==

# Double click the '''Jupyter''' folder on the left. If you do not see it, click [[File:Ana23020.png|frameless]]
## If you did it correctly, you see the following: [[File:Ana23019.png|frameless]]
# When you double click the Jupyter folder, you should see the following: [[File:Ana23021.png|frameless]]
## Each of these folders represents a different Python module and they contain short working Jupyter programs.
# Now, let us double click on the folder '''nglview'''. This Python module allows you to visualize macromolecules.
## If you did it correctly, it should look like:[[File:Ana23022.png|frameless]]
## nglview01, nglview02, nglview03, etc. are folders containing working sample programs.
# Double click on '''nglview01'''
## If you did it correctly, it should look like:[[File:Ana23023.png|frameless]]
# Double click on [[File:Ana23025.png|frameless]]
# If you did it correctly, you should get the following: [[File:Ana23026.png|frameless]]
# At the top left, click [[File:Ana23027.png|frameless]]
# When get prompted to restart the kernel, click '''Yes'''.
## If everything is working correctly, you should get the following output: [[File:Ana23028.png|frameless]]
# '''rdkit''' is another Python module to test to see if your install worked properly.
#if you want to use the '''rpy2''' Python module, you need to install R and R-studio separately from anaconda..

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