└── README.md


/README.md:
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  1 | ## See the <a href="https://github.com/Bioconductor/BiocGithubHelp/wiki/">wiki</a> for notes and tips for using github with Biocondcutor
  2 | <!--
  3 | Every bioc/fhcrc project (including this one, the githubCribsheet) is a separate repository maintained under 
  4 | 
  5 |    https://github.com/Bioconductor
  6 |    
  7 | ### Create your own project (aka repository, or 'repo'):
  8 | 
  9 |  * Register as a user:  https://github.com/signup/free
 10 |  * Send an email to pshannon AT fhcrc.org so that I can give you permissions to create your repo under Bioconductor.
 11 |  * Go to https://github.com/Bioconductor.  Sign in.
 12 |  * Create your new repo by clicking on the leftmost of the three buttons you will find at the top right corner of the page. 
 13 |  It has a '+' on it.
 14 |  * This takes you to a new page where you will be asked to name your project.
 15 |  * On this same page you can edit your repo's <b>README.md</b> which (like this file you are currently reading) records the central documentation for your project.
 16 |  * Save your changes to README.md by clicking on the <b>Commit Changes</b> button found at the bottom right corner of the page.
 17 | 
 18 | ### Setup your computer for git 
 19 |   * <code>git config --global user.name  "your.github.account.name"
 20 |   * <code>git config --global user.email "you@place.com"</code>
 21 |   * configure the <b>credential.helper</b>. Alas, this step differs by operating system because passwords are saved in different ways on osx, linux and windows.   Please get the right instructions for your computer at https://help.github.com/articles/set-up-git
 22 |  
 23 | 
 24 | ### Clone the project onto your own computer
 25 | 
 26 |  * cd toSomeDirectoryOfYourChoice
 27 |  * <code> git clone https://github.com/Bioconductor/githubCribsheet.git</code> with these results
 28 |      * a <b>local repo</b> is created 
 29 |      * a <b>working copy</b> is created
 30 |      * thus <b>three</b> versions of the code exist
 31 | 
 32 | ### Using SSH keys
 33 |  * If you want to use ssh keys instead of https to connect, see this guide: https://help.github.com/articles/generating-ssh-keys
 34 |  * The command to clone the project is then <code>git clone git@github.com:Bioconductor/githubCribsheet.git</code>
 35 | 
 36 | ### Overview of basic operations
 37 | 
 38 |  * Making changes to your <b>working copy</b> propagate them to <b>BOTH</b> of your repos:
 39 |     * Add some text to REAMDE.md, whose contents you originall created at the github website
 40 |     * git diff README.md will report differences between your <b>local repo</b> and your <b>working copy</b>
 41 |     * update the <b>local repo</b>:  
 42 |         <code> git commit -m "added one line, modifying my local working copy" README.md</code>
 43 |     * update <b>github</b>: 
 44 |         <code> git push</code>
 45 |     * make sure your <b>local repo</b> and <b>working copy</b> have a record of the update 
 46 |       you just did to the <b>github repo</b>:   <code>git pull</code>
 47 | 
 48 |   
 49 | ### Add a user to your project
 50 | 
 51 |  * The new user needs a github login id
 52 |  * From the project home page, click the <b>Admin</b> button
 53 |  * Click the <b>Teams</b> button
 54 |  * Click the <b>Owners</b> button
 55 |  * Enter the new user's github id
 56 | 
 57 | ### From SVN to git and back ??
 58 | 
 59 | Does this work? Who knows.
 60 | 
 61 | I explored git / svn a little last night. It seems there is 'git svn'
 62 | (separate from git but widely available), and that steps might be
 63 | 
 64 | 1. Make a repository on github, e.g., http://github.com/mtmorgan/test
 65 | 
 66 | 2. clone the svn repository locally
 67 | 
 68 |   git svn clone \
 69 |       https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graph
 70 | 	  
 71 | This pulls in all the revision history but I think instead it might
 72 | make sense to limit that (e.g., to the last time the version was
 73 | bumped during a release) by making a directory, initiating a git
 74 | repository, fetching a particular revision from svn, and then rebasing
 75 | to the current version
 76 | 	  
 77 |     mkdir graph && cd graph
 78 |       git svn init \
 79 |           https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graph
 80 |     git svn fetch -r64680
 81 | 	git svn rebase
 82 | 				  
 83 | and then I see
 84 | 				  
 85 | 	$ git log --oneline
 86 | 	4aea3d4 The following previously deprecated functions have been made
 87 | 	b11e47e bumped version numbers after creating 2.10 branch
 88 | 				  
 89 | 3. add information about the git repository
 90 | 
 91 |     git remote add origin \
 92 | 	    http://github.com/Bioconductor-mentored/graph.git
 93 | 		
 94 | 4. push the svn clone to github
 95 | 
 96 |     git push -u origin master
 97 |   
 98 | this gets us a github repository with a snapshot of our svn; my
 99 | handiwork is at
100 |   
101 |     https://github.com/mtmorgan/test
102 | 	
103 | We could then git going on all of our revisions and finally...
104 | 	
105 | 5. When done and ready to send back to Bioconductor's svn tree
106 | 	
107 | 	git svn dcommit 
108 | 
109 | -->
110 | 


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