MoinMoin, Sshfs, Git

MoinMoin lets you publish Easy-To-Read web pages and fosters Collaboration

• Try it Now - WikiSandBox

  • Don't hesitate and write something - it's just a sand box.
• To Export pages as PDF

  1. Click on More Actions

  2. Click on Print View

  3. Use your browser to "Print" into a PDF or a PS file

     • The .ps file can be later converted to PDF with the ps2pdf command, which is part of Debian's gs-common package

Sshfs lets you control When and Where your files are mounted

• Important improvements are on their way Re: Deploying SSHFS on workstations instead of NFS

• Mount

  • mkdir bio
    sshfs biocluster: bio

• Un-mount

  • fusermount -u bio
    rmdir bio

• My first Debian 4.0 tested Beta version of a ...

  1. Script that mounts Biocluster when you open your first terminal - Source Code

  2. Script that un-mounts Biocluster when you close your last terminal - Source Code

  3. Bashrc portion that invokes the two scripts - Source Code

Git is More Intuitive, Faster, and more Reliable than CVS and Subversion

I. Starting a Version Controlled Project

• Log-in with X11 forwarding enabled

  • ssh -Y biocluster

• Start your project

  • I create a simple .tree file that can be visualized here http://bioinfo.ucr.edu/projects/TreeBrowse/

    mkdir best-project-of-the-year
    cd !$
    echo "#A very small tree"             > small.tree
    echo "((A:0.35574,B:0.46298):0.218);" >> small.tree
    echo ""                               >> small.tree

• Create an empty Git repository

  • The complete repository will be stored in the .git directory.

    git init
    ls -a # Can you see the .git directory?

• Individually select the files that will be part of the Original Commit to the repository

  • git add small.tree

• Perform the Original Commit

  • When you run this command a text editor will open. Write some simple comment, save, and exit.

    git commit

• Now, let us make this commit a branch named "original"
  • Note: Even though this will create a new branch, we will continue the development on the "master" branch

    git branch original

• So the original small.tree looks like this

  • 

II. Adding some data

• Add some lines to small.tree

  • echo "# Annotations"            >> small.tree
    echo -e "A\t\tred\t\thttp://" >> small.tree
    echo -e "B\t\tred\t\thttp://" >> small.tree

• Add and commit the new changes

  • git add small.tree ; git commit

• Repeat if you need to add more changes
• Now the commited small.tree looks like this

  • 

III. Making a branch and Stepping Back

• List all branches

  • The current branch is marked with an asterisk (*)

    git branch

• Save your current work into a separate branch

  • git branch red

• Open the graphical Git repository browser

  • The --all argument enables visualizing all existing branches

    gitk --all&

  • You will see something like this

    • 

• Step back to the Original Commit

  • Instead of the branch name "original" you put the SHA1 IDs that you can get from the graphical repository browser

    git reset --hard original

  • Now, gitk will show something like this

    • 

• In graphical Git repository browser, click File->Update or press F5

IV. Changing some data

• Open small.tree in a text editor

  • vi small.tree

• Change

  • ((A:0.35574,B:0.46298):0.218);

    to

    ((C:0.35574,D:0.46298):0.7, (A:0.35574,B:0.46298):0.218);

• Close the text editor

  • Now the small.tree is has some structural changes (notice how there is no red, because we did a git reset)

    • 

• Add and commit the new changes

  • git add small.tree ; git commit

  • Now, gitk will show something like this

    • 

• Repeat if you need to change more data

V. Looking at the branches and Merging one into another

• Look at all the branches (you should at least have "master", "original", and "red")

  • git branch

• Take a look at the 'red' branch

  • git checkout red
    git branch     # the branches
    cat small.tree # the data

• Take a look at the 'master' branch

  • git checkout master
    git branch     # the branches
    cat small.tree # the data

• Merge the "red" branch into the "master" (current) branch

  • git merge red
    cat small.tree  # the results of the merge

• In graphical Git repository browser, click File->Update or press F5

  • Now, gitk will show something like this

    • 

  • Do you see how the new commit was created to show that there was a merge?

• The two independent changes were automatically merged together, which can be seen in the resulting small.tree:

  • 

VI. Learning more about Git

• The official Tutorial - http://www.kernel.org/pub/software/scm/git/docs/gittutorial.html

• The complete User Manual - http://www.kernel.org/pub/software/scm/git/docs/user-manual.html