CODEWITHSUNDEEP
python-3.xanacondacondasnakemake
Emily
Emily

Reputation: 93

How to install snakemake 4.3.X?

I need to install snakemake 4.3.X (better 4.3.1), which is supported by python 3.5 and python 3.6.

I've downloaded:

Anaconda3-5.2.0-Linux-x86_64.sh, Anaconda3-5.3.1-Linux-x86_64.sh, Anaconda3-2018.12-Linux-x86_64.sh

from https://repo.anaconda.com/archive/

and installed snakemake separately by using command:

./conda install -c bioconda snakemake

the snakemake installed for each are all version 3.13.1.

Which Anaconda is the proper one for installing snakemake 4.3.X (better 4.3.1) ?

Or are there some other better ways to install snakemake 4.3.X?

Thanks a lot.

Upvotes: 2

Views: 1223

Answers (3)

merv
merv

Reputation: 76760

Based on your use case, you should not install Anaconda. Instead, follow the recommendation of Bioconda (the repository that hosts the snakemake package), and install Miniconda.

Next, set up your channel priorities:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Update the base Conda

conda update -n base conda

Then create a new environment for the Snakemake version you require:

conda create -n snakemake_4_3_1 snakemake=4.3.1

In general, try to leave the base environment alone (other than updating conda), and whenever you need something for a particular task or project, create a new environment for it.

Upvotes: 1

FlyingTeller
FlyingTeller

Reputation: 20482

You are probably getting the older version of snakemake due to version conflicts with the pre-installed modules that accompany an anaconda installation. The anaconda installers you have used are rather old (2 years), so you should probably try with a newer version.

This is not guaranteed to work though. it is not about the version of conda, but about the pre-installed modules in base. Dependencies in the anaconda base env can be tricky. The best solution would be to simply create an environment with the specifications that you need:

conda create -n smake -c bioconda snakemake=4.3.1
conda activate smake

Upvotes: 1

Maarten-vd-Sande
Maarten-vd-Sande

Reputation: 3701

Just FYI there are many newer versions, and we are currently at 5.30.1. Anyhow, you should use:

conda install -c bioconda snakemake=4.3.1

But it is probably best to make a new environment.

Take a look at conda: manage environments for more info about how to install different environments. Possibly you also have to add conda-forge as a channel:

conda config --add channels bioconda
conda config --add channels conda-forge

Upvotes: 0

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