U251 glioblastoma cell line data analysis pipeline

Reproducible pipeline of the experiments described in the manuscript "..."

Requirements

• Any 64-bit Linux installation with GLIBC 2.5 or newer (i.e. any Linux distribution that is newer than CentOS 6).
• working heinz executable in your path. Install from [https://github.com/ls-cwi/heinz].
• To visualize the results: examine.jar. Build from [https://github.com/AlBi-HHU/eXamine-stand-alone].

Usage

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 Snakemake

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 u251-ivgpcr-workflow
cd u251-ivgpcr-workflow

Then, download the workflow archive from TODO and unpack it with

tar -xf u251-ivgpcr-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.

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
  

Remarks regarding reproducibility

GO terms and KEGG pathways are snapshots from March 2018. They can be replaced by new, updated versions by deleting the corresponding files in the GO/ and KEGG/ subdirectories. Note, however, that the results of the enrichment process may change.