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Versión command line

Jose R Ortiz Ubarri 1 year ago
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-# maldisoft
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+# Initial Maldisoft cmdline usage tutorial
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-Moving the source to a public repository
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-asa
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+If you are reading this is because you already unpacked the program.
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+If you list the files and directories you will find the directories:
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+```
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+data
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+html
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+```
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+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.
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+For instance for the NIH example:
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+```
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+mkdir data/nih
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+mkdir html/nih
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+```
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+Copy inside `data/nih` the data to be analyzed.
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+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.  
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+Currently:
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+```
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+1257.4
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+1419.5
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+1581.5
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+1743.6
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+1809.7
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+1905.6
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+```
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+To run the program you just need to follow the following syntax in the terminal:
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+```
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+python maldisoft.py peaks.txt html/sample_name/ data/sample_name/*
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+```
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+For the NIH example it would be:
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+```
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+python maldisoft.py peaks.txt html/nih/ data/nih/*
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+```
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+The results should be inside `html/nih`.
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+To open the results page in your computer go to the directory and double click the index.html file.
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+If you have a mac just do:
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+```
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+open html/nih/index.html
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+```
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