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 3.7 (installed by default on most recent
Unix
systems, available from the Python website)gcc
(installed by default on mostUnix
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 installed by default. You have to install a complete distribution of Python that you can download as a MacOSX package from the Python website.
Developer command line tools can also be installed using the following command line in a UNIX terminal
xcode-select --install
From the Mojaves version of MacOSX the C header have to be installed using the following commands
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
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 theORG.asm
directory itself after the installation by theget-orgasm.py
.The other solution is to add the
export/bin
directory located in theORG.asm
directory to thePATH
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.