This page explains how to install the core package of the Regulatory Sequence Analysis Tools (rsat-core) via the conda package manager.
The rsat-core package contains the RSAT command line tools, but no web server or web services.
The conda package rsat-core is available on the anaconda server, in the bioconda channel:
The package has been compiled for Linux and Mac OS X.
It is not directly available as a conda package for Windows, but it could easily be included in a Docker or Singularity container.
This tutorial assumes that the conda package manager is installed on your operating system.
If it is not the case, you can easily install miniconda3. Note that for this it is not necessary to have admin rights.
For Mac OS X conda can now be installed with the standard Mac OS X package installer.
It may be convenient to create a specific conda environment rather than in the default environment.
Advantage: RSAT and all its dependencies are isolated from the other packages installed on your operating system. This may avoid conflicts between incompatible versions of languages or libraries required by other conda packages.
Inconvenient: the installation may take more space on your storage device since all the dependencies have to be installed in the rsat-specific environment folder.
If you prefer to install rsat-core in the basic conda environment, just skip this section.
Check that the environment has well been created
We will now activate the newly created conda environemnt rsat and check its package content.
The name of the current conda environment should appear at the beginning of your prompt, for example:
(rsat) %
In principle, at this stage, the environment should contain no package since we just created it. We can check this by listing the packages.
In the 2020.01.04 release, some Perl libraries are still missing from conda.
We will soon package them for conda. In the meantime, it is easy to install them manually using cpan (especially if you created a conda environment for rsat, in which case you don’t need admin rights to install Perl modules in the environment).
First, if not done yet, you need to activate the conda environment where rsat-core has been installed.
## Activate the conda environment
##
## Choose either base or rsat depending on your configuration
conda activate
conda activate rsatWe can now install the Perl modules with cpan. At the first usage, cpan might ask you which install mode you prefer between local::lib, sudo or manual. Simply type the enter key to choose the default (local::lib), in order to install the modules in the same environment as your rsat-core package.
## Statistics::Distributions exists in conda but for some reason it is not working
cpan install Statistics::Distributions
## Email::Sender::Simple is required for the Web server + some particular scripts
cpan install Email::Sender::Simple
## Required for matrix-clustering
cpan install Parallel::ForkManager
cpan install MCE::Shared
## For SOAP::WSDL Web services
cpan install SOAP::WSDL
cpan install XML::Compile::SOAP11
cpan install XML::Compile::WSDL11
cpan install XML::Compile::Transport::SOAPHTTPWe can perform a quick test of the rsat-core package.
The rsat command enables to run all the RSAT tools as sub-commands. We can list them with the option --list, or get a short description with the option --help.
The help page of an RSAT command can be obtained by running
rsat [subcommand] -h
For example:
Generate 3 random sequences of length 100.
Generate random sequences and send them as input to oligo-analysis to count the dinucleotide occurrences. Note that the result of an RSAT command can be directly used as input by another command with the pipe symbol |.
The path of the RSAT components depends on your local configuration of conda.
You can find them as subfolders of the conda path, which may itself be generic (base environment) or specific to rsat (rsat environment).
The rsat command is found in the bin directory, together with some RSAT compiled programs (e.g. count-words, matrix-scan-quick, variation-scan). All the programs found in this bin directory are automatically in your path as soon as you activate conda.
The two following commands should in principle return the same path.
Additional files of the RSAT suite are found in the folder share/rsat of the conda directory.
This includes Perl, python, R scripts, makefiles, as well as RSAT configuration files.
RSAT includes a set of tests for different commands, which can be run individually via a makefile.
This displays the list of make targets, which can be called individually by appending them to the previous command. For example, we can run the target randseq in order to test the RSAT program random-seq.
This will generate a random sequence, store it in a local file, and display the path on the result. The same can be done for each other target. The full RSAT command is systematically displayed, which indicates the parameters used for some typical analyses.
The target all runs all the test commands (this can take some time, because it includes downloading the yeast genome, running the peak-motifs workflow, …).
## Before: the individual RSAT Perl and python scripts are not in the path
which random-seq ## a Perl script
which random-motif ## a python script
## Load the bashrc file with RSAT environment variables
cd $CONDA_PREFIX/share/rsat
source RSAT_config.bashrc
## After: the Perl and python scripts are now in the path
which random-seq ## a Perl script
which random-motif ## a python scriptAfter having loaded RSAT_config.bashrc, the commands are avaiable in the path, and can thus be invoked directly (e.g. running random-seq -l 100 would do the same as rsat random-seq -l 100).
To uninstall rsat-core, you should simply remove the package from conda. The way to proceed depends on whether you installed rsat-core in a specific conda environment (rsat) or in the base environment.