/bioconda-paper

Data analysis related to the bioconda paper

Primary LanguagePythonMIT LicenseMIT

DOI Snakemake

Data analysis for the Bioconda paper

This Snakemake workflow automatically generates all results and figures from the Bioconda paper.

Requirements

Any 64-bit Linux installation with GLIBC 2.5 or newer (i.e. any Linux distribution that is newer than CentOS 6). Note that the restriction of this workflow to Linux is purely a design decision (to save space and ensure reproducibility) and not related to Conda/Bioconda. Bioconda packages are available for both Linux and MacOS in general.

Usage

This workflow can be used to recreate all results found in the Bioconda paper.

Step 1: Setup system

Variant a: Installing Miniconda on your system

If you are on a Linux system with GLIBC 2.5 or newer (i.e. any Linux distribution that is newer than CentOS 6), you can simply install Miniconda3 with

curl -o /tmp/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash /tmp/miniconda.sh

Make sure to answer yes to the question whether your PATH variable shall be modified. Afterwards, open a new shell/terminal.

Variant b: Use a Docker container

Otherwise, e.g., on MacOS or if you don't want to modify your system setup, install Docker, run

docker run -it continuumio/miniconda3 /bin/bash

and execute all the following steps within that container.

Variant c: Use an existing Miniconda installation

If you want to use an existing Miniconda installation, please be aware that this is only possible if it uses Python 3 by default. You can check this via

python --version

Further, ensure it is up to date with

conda update --all

Step 2: Setup Bioconda channel

Setup Bioconda with

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

Step 3: Install bioconda-utils and Snakmake

Install bioconda-utils and Snakemake >=4.6.0 with

conda install bioconda-utils snakemake

If you already have an older version of Snakemake, please make sure it is updated to >=4.6.0.

Step 4: Download the workflow

First, create a working directory:

mkdir bioconda-workflow
cd bioconda-workflow

Then, download the workflow archive from https://doi.org/10.5281/zenodo.1068297 and unpack it with

tar -xf bioconda-paper-workflow.tar.gz

Step 5: Run the workflow

Execute the analysis workflow with Snakemake

snakemake --use-conda

Please wait a few minutes for the analysis to finish. Results can be found in the folder figs/. If you have been running the workflow in the docker container (see above), you can obtain the results with

docker cp <container-id>:/bioconda-workflow/figs .

whith <container-id> being the ID of the container.

Known errors

  • If you see an error like

    ImportError: No module named 'appdirs'
    

    when starting Snakemake, you are likely suffering from a bug in an older conda version. Make sure to update your conda installation with

    conda update --all
    

    and then reinstall the appdirs and snakemake package with

    conda install -f appdirs snakemake
    
  • If you see an error like

    ImportError: Missing required dependencies ['numpy']
    

    you are likely suffering from a bug in an older conda version. Make sure to update your conda installation with

    conda update --all
    

    and then reinstall the snakemake package with

    conda install -f snakemake