Most of the tools need some requirements. Some need lot of requirements: Python or R libraries in specific version, the last brand new compilator, or simply a newer one (GCC > 4.4.7), ... Often, thoses dependencies are not compatibles with what we already have on our system or between them.
At ABiMS, it will allow us to install tools within some dedicated and isolated environments. Specially those which require some newer version of GCC 4.4.7.
Note that all software are not provided by Conda. Meanwhile, ABiMS is contributing to add package in Conda through the GitHub repository Bioconda.
We installed 2 versions of Miniconda based on Python 2.7 or Python 3.5. We will install software within miniconda2 or miniconda3 depending of that Python version.
- Conda is not directly in the system $PATH to avoid troubles with existing system libraries and binairies.
- We will always try to provide some isolated environments around the software
Using a Conda environment is quite simple. Firstly you have to activate the environment, secondly use the wanted program(s), and finally restore the default environment.
In this example, we will use programs from stacks-1.45 which are installed into a miniconda2 (i.e. Python 2) environment.
In a script, a terminal or a qlogin, we just have to type the following and program(s) from the Conda env. will appear in the our $PATH.
source $CONDA2/activate stacks-1.45
Now we can use programs from the Conda environment. Here we display the version of cstacks:
cstacks --version # Must return cstacks 1.45
When we have finished, we go back in the default environment with the following command:
source $CONDA2/deactivate stacks-1.45
If you need to use to an environment based on Python 3 instead of Python 2, you have to replace $CONDA2 by $CONDA3.
- Because, those environments isotate the software. The other Python, R or Perl libraries which are installed on the system are not availables within the Conda environment. If it is an issue for you, let us know firstname.lastname@example.org
Tips and Tricks
Before using those commands, you need to type in your terminal/qlogin one of the following command:
$ conda2activate #for miniconda2
$ conda3activate #for miniconda3
When finished, do not forget to go back to unload the environment.
$ conda2deactivate #for miniconda2
$ conda3deactivate #for miniconda3
To know if a tools is avalable though Conda
$ conda search mu_tool
To list all the Conda environments already installed
$ conda env list