Installation instructions

README.md

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 # Chiplot-analyze
 Chiplot-analyze is a utility program designed to take as input 1D traces of the integrated intensity along rectangular boxed shaped regions aligned along either the equator, the meridian, or along a layer line using the program  FIT2D (http://www.esrf.eu/computing/scientific/FIT2D/) and saved as “chiplot” files.  Chiplot files are an ASCIII format and are easily readable in various ways. What chiplot-analyze does is take one of these traces and splits into two halves containing symmetrical diffraction patterns from the left or right (if trace is from the equator or a layer line) or top and bottom (if trace is along the meridian). You can then subtract a continuous background for the trace  using a convex hull algorithm and save the background subtracted trace in a new file.  The background subtracted trace can then be input into various peak fitting programs for further analysis. In the Irving lab this is usually the Fityk program (http://fityk.nieto.pl/) which allows defining custom peak functions. The final thing chiplot-analyze can do is to calculate  the centroid and integrated of  user defined diffraction peaks and save the results to a file. The functionality of chiplot-analyze has been incorporated into the MuscleX package (https://github.com/biocatiit/musclex/wiki) which is a recommended replacement for chiplot-analyze.  It is provided as a legacy application for someone wishing to replicate earlier published work.
+
+## Installation
+So far *chiplot-analyze* is only supported for python 2. Make sure to install
+and run it under python 2 environment.
+```
+python -V
+```
+
+### For Linux
+Install *pip* first if you have not. Also, [TkInter][1] is needed.
+```
+sudo apt-get install python-pip python-tk
+```
+Install *chiplot-analyze*.
+```
+sudo pip install chiplot-analyze
+```
+
+### For Windows
+Install *chiplot-analyze*.
+```
+pip install chiplot-analyze
+```
+
+## Running
+Simply run
+```
+chiplot-analyze
+```
+See [Readme.rst][2] for details.
+Find sample input data [here][3].
+
+[1]: https://wiki.python.org/moin/TkInter
+[2]: https://github.com/biocatiit/chiplot-analyze/blob/master/README.rst
+[3]: https://github.com/biocatiit/chiplot-analyze/tree/master/chiplot_analyze/sample