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====== Differences ====== This shows you the differences between two versions of the page.

--- analysis:nsb2017:week1 [2017/07/01 22:27]
mvdm [Setting up GitHub]
+++ analysis:nsb2017:week1 [2018/04/17 15:20] (current)
@@ Line 12: / Line 12: @@
 Resources:
   * Recommended: [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424|Noble, A Quick Guide to Organizing Computational Biology Projects]] ([[http://www.ploscompbiol.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424&representation=PDF|direct link to pdf]]) (yes, yours is one)
-  * Optional: Introduction to version control with %%GitHub%%: [[http://www.youtube.com/GitHubGuides|Youtube videos]],[[http://readwrite.com/2013/09/30/understanding-github-a-journey-for-beginners-part-1|ReadWrite blog]]
+  * Optional: Introduction to version control with %%GitHub%%: [[https://try.github.io/levels/1/challenges/1 |
+ Try Git]] interactive game, [[http://www.youtube.com/GitHubGuides|Youtube videos]],[[http://readwrite.com/2013/09/30/understanding-github-a-journey-for-beginners-part-1|ReadWrite blog]]
   * More Git and GitHub resources: [[http://git-scm.com/book/en/Getting-Started-Git-Basics|more detailed doc pages]], [[http://stackoverflow.com/questions/tagged/git|git tagged questions on StackOverflow]], [[https://github.s3.amazonaws.com/media/progit.en.pdf|Pro Git manual]] (surprisingly readable)
   * Optional: MATLAB documentation on [[http://www.mathworks.com/help/matlab/matlab_env/understanding-file-locations-in-matlab.html|File Locations]] and [[http://www.mathworks.com/help/matlab/matlab_env/what-is-the-matlab-search-path.html#br8ch8o|Search Paths]]
@@ Line 41: / Line 42: @@
 As an alternative, you can navigate to the course repository [[https://github.com/mvdm/nsb2017|web page]] on %%GitHub%%. There, click the button "Clone in desktop", and your %%GitHub%% client should prompt you to accept the clone (tested successfully with Chrome, %%YMMV%%). If this fails, you can [[http://joe.blog.freemansoft.com/2014/04/github-clone-to-desktop-with-windows.html|drag]] the URL from your browser into your %%GitHub%% client.
-Now, verify that the above steps have resulted in the creation of a ''nsb2017'' folder with various subfolders and files in it, indicating that you have a local copy of the codebase. Because Git is tracking the contents of this folder, it is now easy to "pull" the latest version from %%GitHub%%, either from the command line:
+Now, verify that the above steps have resulted in the creation of a ''nsb2017'' folder with various subfolders and files in it, indicating that you have a local copy of the codebase. Because Git is tracking the contents of this folder, it is now easy to "pull" the latest version from %%GitHub%%, either from the command line (after you ''cd'' into the ''nsb2017'' folder):
 <code>
@@ Line 93: / Line 94: @@
 restoredefaultpath; clear classes; % start with a clean slate
-cd('D:\My_Documents\GitHub\nsb2017\shared'); % or, wherever your code is located -- NOTE \shared subfolder!
+cd('D:\My_Documents\GitHub\nsb2017\code-matlab\shared'); % or, wherever your code is located -- NOTE \shared subfolder!
 p = genpath(pwd); % create list of all folders from here
 addpath(p);
-cd('D:\My_Documents\GitHub\FieldTrip'); % or whatever you chose, obviously
+% can optionally add FieldTrip here when needed (commented out for now)
-ft_defaults;
+% cd('D:\My_Documents\GitHub\FieldTrip'); % or whatever you chose, obviously
+% ft_defaults;
+% rmpath('D:\My_Documents\GitHub\GitHub\fieldtrip\external\signal\') % needed to preserve use of MATLAB filtfilt.m
 </code>
 This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories.
-:!: When setting your path in MATLAB to add the ''shared'' folder only and //not// the parent folder ''nsb2017''. Adding the entire nsb2017 folder will result in an error when you try to run the LoadCSC command later in the module:
+:!: When setting your path in MATLAB to add the ''shared'' folder only and //not// a parent folder such as ''nsb2017''. Adding the entire ''nsb2017'' folder will result in an error when you try to run the LoadCSC command later in the module!
 Optional: if you don't like the ''.git'' folders in your path, you can get clever with [[http://www.mathworks.com/help/matlab/matlab_prog/regular-expressions.html|regular expressions]] to remove these:
@@ Line 133: / Line 136: @@
 Next, let's get some data! Go to the NS&B share and find the ''ExampleData'' folder (within the MouseHippocampus folder).
-For this module you will need the ''R016-2012-10-08'' folder (containing data from one recording session), which you can find in the /promoted/R016 folder. A good place to put it is in something like ''D:\data\promoted\'' (Rxxx indicate different rats, followed by the date of each session). As mentioned, in general you want to keep your data separate from your code; for instance, multiple analysis projects may use the same data, so you don't want to duplicate it.
+For this module you will need the ''R016-2012-10-08'' folder (containing data from one recording session), which you can find in the ''\promoted\R016'' folder on the share. Copy this folder onto your own computer. A good place to put it is in something like ''D:\data\promoted\'' (Rxxx indicate different rats, followed by the date of each session). As mentioned, in general you want to keep your data separate from your code; for instance, multiple analysis projects may use the same data, so you don't want to duplicate it.
 The choice of the folder name ''promoted'' indicates that these are data folders for which preprocessing is completed. As will be explained further in Module 2 and others, preprocessing typically includes the renaming of raw data files, annotation, spike sorting, and a few other steps. In general, it is useful to keep promoted data separate from data still in process.

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