From eb33f6a8d4517cccc48c8e91012ae261fe609fae Mon Sep 17 00:00:00 2001 From: Xintian Date: Fri, 23 Mar 2018 23:21:00 -0500 Subject: [PATCH] Installation instructions --- README.md | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/README.md b/README.md index 16d6a58..feb999a 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,37 @@ # 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 \ No newline at end of file