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`_).
To install the the ORGanelle ASeMbler, you need that these softwares are installed on your system:
- Python 3.4 (installed by default on most
Unixsystems, available from the Python website)
gcc(installed by default on most
Unixsystems, 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.
Downloading and installing the ORGanelle ASeMbler¶
> 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.
Once activated you can desactivate the ORGanelle ASeMbler by typing the command
> 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/binbut never move the
ORG.asmdirectory itself after the installation by the
- The other solution is to add the
export/bindirectory located in the
ORG.asmdirectory to the
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