Conda_Environment_instructions.txt

Create Anaconda environment:
- open anaconda navigator
- go to Environments and select Create
- Open the terminal from the Big Arrow


Open a Anaconda Command Prompt from your environment and type:
- cd %CONDA_PREFIX%
- mkdir .\etc\conda\activate.d
- mkdir .\etc\conda\deactivate.d
- type NUL > .\etc\conda\activate.d\env_vars.bat
- type NUL > .\etc\conda\deactivate.d\env_vars.bat


Install Dot
- download from https://graphviz.gitlab.io/_pages/Download/Download_windows.html

Install wget
- download wget from : https://eternallybored.org/misc/wget/  (32bit)

Install md5
- download md5 from https://www.fourmilab.ch/md5/

Add executable to path (Open A Anaconda Command Prompt from your environment)
- Open the file .\etc\conda\activate.d\env_vars.bat (just type "notepad %CONDA_PREFIX%\etc\conda\activate.d\env_vars.bat")

- Add the following lines to the file (make sure to close all the shells before this step)

'''
echo off
set WGET_PATH=C:\Where\the\wget_directory\is ( probably in something like \wget-1.20-win32)
set GRAPHVIZ_PATH=C:\Where\the\graphviz_directory\is\release\bin (probably something like graphviz-2.38\release\bin)
set MD5_PATH=C:\Where\the\md5_directory\is (probably something like \md5)
set PATH=%PATH%;%WGET_PATH%;%GRAPHVIZ_PATH%;%MD5_PATH%;
echo on
'''

Close and run the environment terminal

Install Snakemake
- open anaconda navigator
- open your environment
- select Not Installed from the menu
- Add Channels "bioconda" and "conda-forge" (Channels -> Add)
- Search "snakemake"
- Install "snakemake-minimal" 
- Click on the big arrow and open terminal


Legenda:

cat            -> type
echo 	       -> echo
ls / ll        -> dir
cp             -> copy
touch filename -> copy NUL filename
mv             -> move / rename
mkdir          -> mkdir / md
rm             -> del / erase
echo $PATH     -> PATH