Pre-built Packages

Pre-built (binary) packages are available for the following distributions:

  • Debian (Etch)
  • Ubuntu (Feisty Fawn / Gutsy Gibbon / Hardy Heron)
  • Fedora Core (7, 8)
  • CentOS and Red Hat Enterprise Linux (4, 5)

The build is divided into 5 packages:

  • ecell3 (CLI tools and utilities)
  • ecell3-dev / ecell3-devel (necessary for DM developing)
  • ecell3-session-monitor (GUI session monitor)
  • ecell3-model-editor (GUI model editor)
  • ecell3-tool-launcher (GUI compiler launcher)

Packages for these distributions are placed at downloads.e-cell.org.

Note that the repositories contain several packages of other projects (e.g. libSBML) for convenience.

You can browse the available packages through the very simple indexer from here.

Notes for third-party packages

libSBML

The build system was heavily patched in favor of libtoolized libraries.

  • For deb's, libSBML is provided as 6 separate packages:
    • libsbml2
      libSBML C++ runtime library package.
    • libsbml2-dev
      libSBML C++ development package. Include files, .la files and static library archives (*.a).
    • libsbml2-java
      Java binding of libSBML. JNI part (libsbmlj.so) will be installed in /usr/lib/jni and stub class archive (libsbmlj.jar) in /usr/share/java.
    • libsbml2-perl
      Perl binding of libSBML.
    • python-sbml2
      Python binding of libSBML.
    • libsbml2-examples
      Example sources.
    • libsbml2-docs
      The manual and API reference.
  • For RPM's, libSBML is provided as 5 separate packages:
    • libsbml
      libSBML C++ runtime library package.
    • libsbml-devel
      libSBML C++ development package. Include files, .la files and static library archives (*.a). Contains the manual and API reference.
    • libsbml-java
      Java binding of libSBML. JNI part (libsbmlj.so) will be installed in /usr/lib and stub class archive (libsbmlj.jar) in /usr/share/java.
    • libsbml-perl
      Perl binding of libSBML.
    • libsbml-python
      Python binding of libSBML.

NumPy

  • Basically the same as FC8's except for el4, where blas and lapack dependencies are dropped.

Instruction

Debian / Ubuntu (apt and dpkg based)

Append any one of the following lines to /etc/apt/sources.list.

  • Debian: Etch 
    deb http://downloads.e-cell.org/apt/etch/ etch contrib
  • Ubuntu: Feisty Fawn 
    deb http://downloads.e-cell.org/apt/feisty/ feisty contrib
  • Ubuntu: Gutsy Gibbon 
    deb http://downloads.e-cell.org/apt/gutsy/ gutsy contrib
  • Ubuntu: Hardy Heron 
    deb http://downloads.e-cell.org/apt/hardy/ hardy contrib

Next, run apt-get update to update the local copies of package databases.

Finally, just type 

apt-get install ecell3

to see everything gets installed without difficulties anymore :)

Fedora Core / Cent OS (yum and rpm based)

Save any one of the following content to /etc/yum.repos.d/ecell.repo .

  • CentOS: Version 4, 5 
    # Name: E-Cell RPM Repository for Red Hat Enterprise 4, 5
# URL: http://downloads.e-cell.org/
[ecell]
name = Red Hat Enterprise $releasever - E-Cell
baseurl = http://downloads.e-cell.org/yum/el$releasever/$basearch
enabled = 1
protect = 0
gpgcheck = 0
  • Fedora Core: Version 7, 8 
    # Name: E-Cell RPM Repository for Fedora Core
# URL: http://downloads.e-cell.org/
[ecell]
name = Fedora Core $releasever - E-Cell
baseurl = http://downloads.e-cell.org/yum/fc$releasever/$basearch
enabled = 1
protect = 0
gpgcheck = 0

And then type 

yum install ecell3

to get your E-Cell installation out of the repository.