Update the README directory

README.md

@@ -1,17 +1,16 @@
-# Initial Maldisoft cmdline usage tutorial
+# Maldisoft cmdline usage tutorial
 
-If you are reading this is because you already unpacked the program.
 
-If you list the files and directories you will find the directories:
+Create the data and html directories:
 
 ```
-data
-html
+mkdir data
+mkdir html
 ```
 
-In the data directory you **MUST** create a sub directory with the data that you want to analyze together and then create a directory inside html where the results will be written.
+Inside the `data` directory you **MUST** create a sub directory for the data that you want to analyze together. Then, inside the `html` directory you MUST also create a subdirectory where the results will be written.
 
-For instance for the NIH example:
+For example if you plan to analize data from the database nih:
 ```
 mkdir data/nih
 mkdir html/nih
@@ -19,7 +18,7 @@ mkdir html/nih
 
 Copy inside `data/nih` the data to be analyzed.
 
-The list of peaks that you want to analyze is inside the file peaks.txt.  If you want to remove or add a new peak just follow the same format that is inside the file.  
+The list of peaks that you want to analyze is inside the file peaks.txt.  If you want to remove or add a new peak just follow the same one column format that is inside the file.  
 
 Currently:
 
@@ -35,19 +34,19 @@ Currently:
 To run the program you just need to follow the following syntax in the terminal:
 
 ```
-python maldisoft.py peaks.txt html/sample_name/ data/sample_name/*
+python2 maldisoft.py peaks.txt html/sample_name/ data/sample_name/*
 ```
 
 For the NIH example it would be:
 ```
-python maldisoft.py peaks.txt html/nih/ data/nih/*
+python2 maldisoft.py peaks.txt html/nih/ data/nih/*
 ```
 
 The results should be inside `html/nih`.
 
 To open the results page in your computer go to the directory and double click the index.html file.
 
-If you have a mac just do:
+If you have an apple machine just do:
 
 ```
 open html/nih/index.html