How To Install snakemake on Fedora 34
snakemake is Workflow management system to create reproducible and scalable data analyses
Introduction
In this tutorial we learn how to install snakemake on Fedora 34.
What is snakemake
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
We can use yum or dnf to install snakemake on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install snakemake.
Install snakemake on Fedora 34 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install snakemake using dnf by running the following command:
sudo dnf -y install snakemake
Install snakemake on Fedora 34 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install snakemake using yum by running the following command:
sudo yum -y install snakemake
How To Uninstall snakemake on Fedora 34
To uninstall only the snakemake package we can use the following command:
sudo dnf remove snakemake
snakemake Package Contents on Fedora 34
/usr/bin/snakemake
/usr/bin/snakemake-bash-completion
/usr/lib/python3.9/site-packages/snakemake
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/PKG-INFO
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/SOURCES.txt
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/dependency_links.txt
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/entry_points.txt
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/not-zip-safe
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/requires.txt
/usr/lib/python3.9/site-packages/snakemake-6.6.0-py3.9.egg-info/top_level.txt
/usr/lib/python3.9/site-packages/snakemake/__init__.py
/usr/lib/python3.9/site-packages/snakemake/__main__.py
/usr/lib/python3.9/site-packages/snakemake/__pycache__
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/usr/lib/python3.9/site-packages/snakemake/ruleinfo.py
/usr/lib/python3.9/site-packages/snakemake/rules.py
/usr/lib/python3.9/site-packages/snakemake/scheduler.py
/usr/lib/python3.9/site-packages/snakemake/script.py
/usr/lib/python3.9/site-packages/snakemake/shell.py
/usr/lib/python3.9/site-packages/snakemake/sourcecache.py
/usr/lib/python3.9/site-packages/snakemake/stats.py
/usr/lib/python3.9/site-packages/snakemake/unit_tests
/usr/lib/python3.9/site-packages/snakemake/unit_tests/__init__.py
/usr/lib/python3.9/site-packages/snakemake/unit_tests/__pycache__
/usr/lib/python3.9/site-packages/snakemake/unit_tests/__pycache__/__init__.cpython-39.opt-1.pyc
/usr/lib/python3.9/site-packages/snakemake/unit_tests/__pycache__/__init__.cpython-39.pyc
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates/__init__.py
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates/__pycache__
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates/__pycache__/__init__.cpython-39.opt-1.pyc
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates/__pycache__/__init__.cpython-39.pyc
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates/common.py.jinja2
/usr/lib/python3.9/site-packages/snakemake/unit_tests/templates/ruletest.py.jinja2
/usr/lib/python3.9/site-packages/snakemake/utils.py
/usr/lib/python3.9/site-packages/snakemake/workflow.py
/usr/lib/python3.9/site-packages/snakemake/wrapper.py
/usr/share/doc/snakemake
/usr/share/doc/snakemake/README.md
/usr/share/licenses/snakemake
/usr/share/licenses/snakemake/LICENSE.md
References
Summary
In this tutorial we learn how to install snakemake on Fedora 34 using yum and dnf.
