Installation and updating¶

For an easy installation process we recommend using Conda. All necessary steps are described in detail below.

Installing on a fresh Ubuntu system using Conda¶

The following installation steps where tested on ubuntu:22.04. We recommend using the package and environment manager Conda for an easy installation. It can be downloaded and installed with Anaconda. After installing anaconda add the channels anaconda-forge and bioconda by entering the following commands in your terminal:

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

To avoid package conflicts we recommend creating a conda environment for READemption based on Python 3.9:

conda create -n "reademption" python=3.9

Afterwards activate the environment:

conda activate reademption

Now you can install the READemption conda package that includes READemption and all its dependencies (e.g. segemehl and DESeq2):

conda install -c till_sauerwein reademption -y

READemption is ready to use and you can start your own analysis or try one of our example analyses

Installing on a fresh Ubuntu system using pip¶

The following installation steps where tested on ubuntu:22.04.

Requirements¶

READemption 2.0.0 was developed using Python 3.9 and the user is advised to run READemption with this or a higher version. In any case setuptools and pip should be available on the system in order to make the installation easy. READemption uses the short read mapper segemehl for the mapping and this software needs to be installed. The bioconductor package DESeq2 is necessary for the subcommand deseq which performs differential gene expression analysis. All other requirements are installed via pip’s READemption package. Don’t worry - in the following the installation of all these requirements will be covered.

1. Installing all required Debian/Ubuntu packages¶

Before starting it is a good idea to update the package list:

sudo apt-get update

Now you can install the packages:

sudo apt-get install python3 python3-setuptools python3-pip python3-matplotlib cython3 zlib1g-dev  make libncurses5-dev r-base libxml2-dev

Some comments:

Python version 3.9 and higher is recommended
cython is required for pysam
make, libncurses5-dev and zlib1g-dev are needed for segemehl
libxml2 is required for the installation of some of the R-packages

2. Install segemehl (version 0.3.4)¶

curl https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/segemehl-0.3.4.tar.gz > segemehl-0.3.4.tar.gz
tar segemehl-0.3.4.tar.gz
cd segemehl_*/segemehl*/ && make all && cd ../../

Copying the executable to a location that is part of the PATH e.g /usr/bin/ …

sudo cp segemehl-0.3.4/segemehl-0.3.4/segemehl.x /usr/bin/segemehl.x

… or the bin folder of your home directory:

mkdir ~/bin
cp segemehl-0.3.4/segemehl-0.3.4/segemehl.x ~/bin

Alternatively, segemehl can be installed via conda:

conda install -c bioconda segemehl=0.3.4

3. Install DESeq2¶

Start R:

and install the DESeq2 package inside of the interactive command line interface. You might be asked to confirm the installation path:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("DESeq2")

Leave R:

quit(save = "no")

Install READemption and it’s dependcies¶

Now you can use pip to install READemption and further python packages:

sudo pip install READemption

Voilà! You should now be able to call READemption:

reademption -h

Installing on a Apple OS X¶

(Many thanks to Lei Li for contribution this part!)

1. Installing all required software/packages¶

To download and install Python 3 follow the instruction at this download page.

Download and install xcode (page) and R (download links are on the frontpage).

To install pip open a terminal and run

curl -O https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py python3 ez_setup.py # download and install pip
curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
python3 get-pip.py

Install matplotlib:

pip3 install matplotlib

2. Installing segemehl, DESeq, pysam and READemption¶

The remaining installation steps are the same as descibed above. Just open a terminal and run the commands.

Updating READemption¶

Once you have installed READemption as described above you can easily upgrade it to the newest version by running

pip3 install --upgrade READemption