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Obtaining the software

Source code is now under GIT version control and is hosted online at http://github.com/bioteam/xml-qstat.

There are many ways to access, browse, clone or download the codebase, including methods for directly downloading .tar.gz or .zip archives for people who do not wish to install (or can't use) git clients internally.

Official Releases

There are no official releases or tags yet.

Starting with git

Go to a clean starting place (eg, your home directory):

$ cd $HOME

Clone the repository without checking out anything just yet and we'll also specify 'github' as the name of the remote repository that we'll be tracking:

$ git clone --no-checkout --origin github http://github.com/bioteam/xml-qstat.git

We now change to the newly created directory:

$ cd xml-qstat/

Since we haven't checked out any files, the only thing in the directory will be the .git/ hidden directory:

$ ls -a
./  ../  .git/

Listing all of the git branches should look like this ('*'; indicates the currently active branch):

$ git branch -l -a
* master
  github/HEAD
  github/master

Now we are ready to start our own branch, which we'll setup without tracking the remote branch. This is an important point. By creating a non-tracked branch, we can avoid worrying about clobbering any of our custom settings with future updates.

$ git checkout --no-track -b site github/master

For general cleanliness, we'll also remove the tracked branch master, but it can always be reinstated later if desired:

$ git branch -d master
Deleted branch master.

We can now check that everything is as it should be:

$ git status
# On branch site
nothing to commit (working directory clean)

Since we are on our own branch (site), we can make changes independent of the upstream branches (github/master).

The first thing we'll do is adjust the paths to suit our installation. Depending upon your final configuration, you may not need to adjust all of the following files:

 

  build-xmlqstat-jar.sh
  init-scripts/cocoon
  init-scripts/httpi
  init-scripts/xmlqstat-cacher
  scripts/jobinfo
  scripts/xmlqstat-cacher.pl

You should also adjust the xmlqstat/config/config.xml to reflect your site (perhaps with your own logo image). If you are using the FlexLM integration (qlicserver), you should also symlink the cache directories at this time under xmlqstat/cache-{clusterName}.

To preserve these initial edit ting changes thus far, some of the following commands will be useful.

git status

check the current of things

git add -u

stage updated files for the next commit

git add file1 .. fileN

stage new files for the next commit

git commit

commit the changes

git commit --amend

amend to the previous commit

git log

view the commit log

At any time we can also fetch the newest version, without affecting our working directory whatsoever:

git fetch github

fetch the lastest version

git log --stat --no-merges github/master ^HEAD

view the changes in github/master but not in our branch

Provided that our working directory is clean (no uncommitted changes), we can merge in any upstream changes:

$ git merge github/master

This normally merges without problems, except when you have changed exactly the same lines as have been changed in the github/master. You'll need to resolve such conflicts by hand (git can't really tell who should be right in this situation) and commit the finally resolved versions.