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Code downloads

We use Bazaar-NG for version control (reasons why we choose Bazaar). You'll have to install Bazaar and then do bzr get whatever.url.we.provide to get the code. Other forms might be available (e.g., tar.gz files with the R packages), but by using bzr you'll get the most recent code. Moreover, this makes it simpler to collaborate with us, send patches, etc.

The code for the project is also mirrored at Launchpad. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail).

Asterias common

There are some installation instructions common to all Asterias web applications, scripts that might help you with the installation, LAM/MPI controlling scripts, etc. You will need this (or something similar) for all your attempts to install the web-based applications until we can finally provide a working Pylons-based egg installer.

   bzr get


This is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). to clean up the code, to get rid of lots of code duplication, and to make the logic of the programs simpler. But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing:

   bzr get


All the code for ADaCGH. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources:

   bzr get

but if you only want the R package you can just do


(the version might have changed; visit the page and check it out and update if needed).

Pomelo II

All the code for Pomelo II. The C++ can be compiled for stand-alone operation. Download it doing

   bzr get


All the code for SignS. Download it doing

   bzr get


All the code for GeneSrF. Download it doing

   bzr get


All the code for Tnasas. Download it doing

   bzr get


All the code for DNMAD. Download it doing

   bzr get

This differs from the rest of applications both in the language (Perl instead of Python) and some of the internal logic.

IDconverter and IDClight

You know what do do already :-). Please note that we use databases which are not included in the download (they are huge, and they are periodically updated).

   bzr get
   bzr get

Functional Testing:

The Python and R code for functional and regression testing. You will need Funkload for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/ The most recent code is available doing

   bzr get

Please note that comprehensive testing of the Javascript and AJAX functionality for Pomelo II is not included here. Instead, that testing is carried out using Selenium. See the Pomelo Selenium tests page. These tests have been verified with Opera (8.54) under Windows and Linux, Firefox 1.5 (Windows and Linux), Konqueror 3.5 (Linux) and Internet Explorer 1.6 (only Windows). These tests do not run under Opera 9.0 or 9.02 (something strange in the way the JS is processed by Opera).


The R package is available from CRAN in the usual tar.gz and zip formats. The most recent code is available doing

   bzr get

A description of the method implemented in RJaCGH is available as a COBRA Preprint Series Article.


The R package is available from CRAN in the usual tar.gz and zip formats. The most recent code is available doing

   bzr get

A paper that describes one of the methods implemented there is available from BMC Bioinformatics.

Other applications

The rest will be available very soon.

Requirements for the web-based applications:

  • Python 2.4 (and a bunch of standard Python 2.4 packages).
  • A web server (only tested with Apache 1.3)
  • R (2.2.0 or higher), and several R and BioC packages. You might want to take a look at the scripts and, and modify them for your setting. They can help automate downloading and isntalling most of the dependencies.
  • A C/C++ compiler
  • PHP
  • MPI (only tested with LAM/MPI)
  • Sufficient storage space for temporary files (currently project takes about 12 GB, and most of those are temporary files).
  • For IDconverter and IDClight about 20 GB for the pregenerated tables.
  • For load balancing and high-availability of web services: heartbeat and either Linux Virtual Server and ldirectord) or Pound (Pound already monitors the servers).
  • For functional and regression testing: FunkLoad
  • To grab the latest code from our repositories: Bazaar-NG

Installation (web-based applications)

  • Make sure you have installed and downloaded the above programs
  • You need the corresponding R code. For example, for genesrf, install the varSelRF R package, etc.
  • Configure your web server, so that requests for you installation are sent to right place.
  • Get MPI running. For all the applications that use MPI, the universes are started and stopped independently for each.

Asterias common has several files that can be used as examples. Most of the applications call "" and it is likely that you will need to modify the paths. Likewise, the files in Asterias-common provide examples for monitoring applications, logging, etc. Paths here will probably need to be modified. You will also probably need to change the IPs of the hosts of your cluster.

  • LAM/MPI is run by the web server user. We had to change the default shell for our apache user, so it could boot lam universes.

Licenses we use for the code

See the LicensesPage for details, and the first lines of each file you are interested in, since we use either the GPL or the Affero GPL.

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Page last modified on May 16, 2007, at 01:24 PM