Bio-Image Informatics Project

This is the toplevel wiki and project site for the Bio-Image informatics project.

This site contains materials for whole project.

More details can be found in each subproject.

PrefixTrac Site
bisqueBisQue project
infrastructureCBI Infrastructure
tracThe Trac Project

Becoming a wiki/ticket system user

If you are user of the above projects and you wish to comment, add tickets or reports, you will need to register

as a trac user.

Becoming a Developer

Getting Source code for a project

A read-only source repository is here You must use Mercurial in order to download the current source.

You can retreive a read-only copy with

hg clone<project>

read/write access to the source

All of our internal projects use Mercurial for source control. Mercurial is a fast and easy to use source management system.

Once you are enabled you can get copy with

hg clone ssh://<project name>

Further information can be found in UsingMercurial

if you plan on submitting patches directly our archive, you will need to be known to our development server ( We control access based on your ssh key.

We have several ways to let the server know your ssh key.

  1. If you already have ssh access to biodev, follow the instructions here
  2. Or email your public key (usually ~/.ssh/ to kris@… and I will add it.
  3. After you are added.. clone/pull/push simply with (Respository List)
    hg clone ssh://<reponame> 

Adding a project

Several steps must be down to create a working trac+mercurial environement. You can a find a script that covers most cases in infrastructure:wiki:WikiStart. Look for /wiki/bin/make-trac-project.

If you wish to do this by hand, steps are as follows

  1. Create a trac directory (usually under /home/trac/projects/<project>)
  2. Create a mercurial repository (usually under /home/mercurial/repos/<project>') on
  3. cd /home/mercurual/repos/<project> and run hg init
  4. It is a good idea to commit at least one file (i.e. a README).
  5. run trac-admin /home/trac/projects/<project> initenv and answer the questions (hg instead of svn)
  6. Add the intertrac reference to /usr/share/trac/conf/trac.ini
  7. Change the ownership chown -R www-data.www-data /home/trac/projects/<project>
  8. Change the ownership chown -R hg.staff /home/mercurial/repos/<project>
  9. Set the TRAC default permissions with set-default-perm /home/trac/projects/<project>

Modify /home/trac/projects/bioimage/conf/trac.ini adding the new project:

myproject.title = A new project
myproject.url  = /projects/newproject
myproject.compat = false

Other resources

For a complete list of local wiki pages, see TitleIndex.

Last modified 9 years ago Last modified on 02/24/2012 12:38:28 PM