Slivka-bio is a pre-configured instance of a slivka project using conda targeted for bioinformatics. It contains configurations for tools such as Clustal Omega, ClustalW2, Muscle, IUPred, Mafft and more. The goal is to provide (almost) ready to use package which bundles bioinformatic software in one tool. The applications currently available include:
- Clustal Omega
- ClustalW2
- MUSCLE
- T-Coffee
- AACon
- IUPred (sources not included)
- MAFFT
- ProbCons
- MSAProbs
- GlobPlot
- DisEMBL
- JRonn (Java implementation of RONN)
- JPred
The easiest way to install slivka-bio with most of the tools and dependencies is by using a slivka-bio package available from our anaconda channel. If you don't have conda installed on your system, follow the miniconda installation from conda user guide. Then, run
conda create -n '<your-env-name>'
conda activate '<your-env-name>'
conda install -c slivka -c mmwarowny -c bioconda slivka-bioIt will automatically install slivka-bio and bioinformatic tools in the chosen environment. Follow to the configuration section if you need to customise some of the settings.
The recommended way to manage slivka installation and dependencies
is through conda package manager. If you don't have conda installed
on your system yet, follow the miniconda installation instructions
from conda user guide.
Once the conda installation completes, create a new conda environment
with python version 3.10 and activate it. Substitute the environment
name of your choice for slivka if needed.
conda create -n slivka python=3.10
conda activate slivkaMake sure that python executable points to the binary located
in the conda environment.
Next, download and install Slivka python package as well
as slivka-bio configuration files from our github repository.
For the time being, we recommend using the version from the dev branch
until the first stable version is released.
git clone --branch dev --single-branch https://github.com/bartongroup/slivka.git
(cd slivka; python setup.py install)
git clone --branch dev --single-branch https://github.com/bartongroup/slivka-bio.gitKeep in mind that slivka-bio does not include any bioinformatic tools. If you choose this installation route, you need to provide them by yourself.
If you choose to install slivka-bio using conda then all the tools, except IUPred, are automatically installed by conda. However, if you decide to install or update them manually, most them are available from bioconda, my private conda channel - mmwarowny, or are shipped with slivka-bio.
Tools: ClustalO, ClustalW, MUSCLE, T-Coffee, MSAProbs, Probcons, MAFFT and RNAalifold can be installed with conda package manager from the bioconda channel.
You can install each tool running the following commands (remember to activate the conda environment first)
conda config --add channels conda-forge
conda config --add channels bioconda
conda install clustalo clustalw muscle t_coffee msaprobs probcons mafftTools: DisEMBL and GlobPlot as well as a more recent version of T-Coffee for macOS and linux are available from the mmwarowny channel.
conda config --add channels mmwarowny
conda install disembl globplot t_coffeeTools AACon and JRonn are shipped as compiled Java executables and require Java 1.8 or later to be installed on your system. Most system provide Java Runtime Environment out-of-the-box but if it's not the case you can install it using conda.
conda install openjdkIt is highly recommended to install the bioinformatic tools using the package managers. However, if you prefer building bioinformatic tools from the sources and have a full control over the installation process you are free to do so. After the compilation, make sure that the binary location is included in the PATH variable or set the absolute path to the binary in the service configuration file.
Due to the legal limitations, IUPred sources could not be included in
the slivka-bio package nor can be provided through conda.
If you wish to use it, you can download the sources from
iupred website.
Then, place them in bin/iupred directory and run make iupred.
Compiling IUPred requires C compiler, which is a part of the GNU
toolchain, to be installed on your system.
Make sure that make and gcc are available on your system.
On Debian/Ubuntu/Mint they can be installed with
apt-get install make gccOn CentOS/Redhat/Fedora they are available as part of the Development Tools
yum group install "Development Tools"Using homebrew on MacOS
brew install make gccUsing conda package manager
conda install gcc_linux-64 # linux
conda install clang_osx-64 # MacOSFor other operating systems refer to you package manager repositories.
Web Service Gateway Interface is a convention for web servers to forward HTTP requests to python application. Recommeded middleware supported by Slivka include Gunicorn and uWSGI. You need to install one of those (both available as conda packages) to use slivka server. If you want to use other software the wsgi application is located in the wsgi.py module file and is named application.
Slivka-bio configuration is organised into multiple files.
Basic configuration is located in the settings.yaml file
in the repository root directory
The configurations for each service is located in its respective file
in the services folder.
If slivka-bio was installed with conda package manager, the configuration
files are located at $CONDA_PREFIX/var/slivka-bio
For in depth service configuration instructions refer to the slivka documentation.
Slivka depends on MongoDB for exchanging
and storing data.
Ask your system administrator for installation and access to the mongo
database on your system or, if you need user installation only, mongodb
is available through conda in anaconda channel.
Once installed, MongoDB process can be started using mongod command.
More information on available command line parameters and configuration
can be found in the mongod documentation.
Once you finished the configuration step, you can deploy your own slivka server. First, navigate to the slivka configuration directory (the one having settings.yaml in it). Alternatively, you can set SLIVKA_HOME environment variable pointing to that directory. For slivka to operate properly, you need to start its three processes: http server which manager incoming connections, scheduler which collects and dispatches incoming job requests, local-queue which stacks and runs incoming jobs on the local machine.
The three processes are launched using slivka command created during
slivka installation. Alternatively, you can use manage.py script
located in the project directory which automatically sets SLIVKA_HOME
variable when started.
If you have slivka-bio installed as a conda package, use slivka-bio
command instead. All other command line parameters remain the same.
slivka start server [-t TYPE] [-d -p PID_FILE] [-w WORKERS]Starts the HTTP server using WSGI application specified by TYPE.
Allowed values are devel, uwsgi or gunicorn. The specified
application must be installed and available in the PATH.
The development server is always available, but it can't serve more
than one client at the time therefore it's not recommended for production.
If you want to make your server publicly accessible, we recommend running it behind a reverse proxy server. Refer to your wsgi application documentation for more details.
Providing -d flag along with -p PID_FILE starts the process in
background as a daemon and writes its pid to the file.
You can also specify the number of worker processes explicitly. Defaults to twice the cpu-count.
slivka start scheduler [-d -p PID_FILE]Starts the scheduler that collects and dispatches new jobs and monitors their states.
Providing -d flag starts the scheduler as a daemon and -p PID_FILE
specifies the pid file location.
slivka start local-queue [-d -p PID_FILE] [-w WORKERS]This is a default job runner which spawns new jobs as subprocesses on
the local machine. If you specify -d and -p PID_FILE the process
will run as a daemon and write its pid to the specified file.
Additionally, you may specify the number of workers i.e. the number of jobs which can be run simultaneously. Defaults to 2.