Installing the ORGanelle ASeMbler

Availability of the ORGanelle ASeMbler

The ORGanelle ASeMbler is open source and protected by the CeCILL 2.1 license (http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html).

The ORGanelle ASeMbler is deposited on the Python Package Index (PyPI : `https://pypi.python.org/pypi/ORG.asm`_) and all the sources can be downloaded from the metabarcoding.org gitlab server (`https://git.metabarcoding.org/org-asm/org-asm`_).

Prerequisites

To install the the ORGanelle ASeMbler, you need that these softwares are installed on your system:

  • Python 3.4 (installed by default on most Unix systems, available from the Python website)
  • gcc (installed by default on most Unix systems, available from the GNU sites dedicated to GCC and GMake)

On a linux system

You have to take care that the Python development packages are installed.

On MacOSX

The C compiler and all the other compilation tools are included in the XCode application not installed by default. Python3 is not prived by default. You have to install a complete distribution of Python that you can download as a MacOSX package from the Python website.

Downloading and installing the ORGanelle ASeMbler

The the ORGanelle ASeMbler is downloaded and installed using the get-orgasm.py script. This is a user level installation that does not need administrator privilege.

Once downloaded, move the file get-orgasm.py in the directory where you want to install the the ORGanelle ASeMbler. From a Unix terminal you must now run the command :

> python3 get-orgasm.py

The script will create a new directory at the place you are running it in which all the the ORGanelle ASeMbler will be installed. No system privilege are required, and you system will not be altered in any way by the obitools installation.

The newly created directory is named ORG.asm-VERSION where version is substituted by the latest version number available.

Inside the newly created directory all the the ORGanelle ASeMbler is installed. Close to this directory there is a shell script named orgasm. Running this script activate the the ORGanelle ASeMbler by reconfiguring your Unix environment.

> ./orgasm

Once activated you can desactivate the ORGanelle ASeMbler by typing the command exit.

> exit

ORG.asm are no more activated, Bye...
=====================================

System level installation

To install the the ORGanelle ASeMbler at the system level you can follow two options :

  • copy the the ORGanelle ASeMbler script in a usual directory for installing program like /usr/local/bin but never move the ORG.asm directory itself after the installation by the get-orgasm.py.
  • The other solution is to add the export/bin directory located in the ORG.asm directory to the PATH environment variable.

Retrieving the sources of the ORGanelle ASeMbler

If you want to compile by yourself the the ORGanelle ASeMbler, you will need to install the same prerequisite:

> pip3 install -U pip
> pip3 install -U sphinx
> pip3 install -U cython

moreover you need to install any git client (a list of clients is available from GIT website)

Then you can download the

> git clone https://git.metabarcoding.org/org-asm/org-asm.git

This command will create a new directory called org-asm.

Compiling and installing the ORGanelle ASeMbler

From the directory where you retrieved the sources, execute the following commands:

> cd org-asm

> python3 setup.py --serenity install

Once installed, you can test your installation by running the commands of the tutorials.