Installation and updating

Requirements

READemption was started to be developed using Python 3.2 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 subcommands viz_align, viz_gene_quanti, viz_deseq require the Python library Matplotlib. R and the bioconductor package DESeq2 are necessary for the subcommand deseq which performs differential gene expression analysis. Don’t worry - in the following the installation of all these requirements will be covered.

Installing on a fresh Ubuntu system

The following installation procedure was tested on a Amazon AWS t1.micro instance with Ubuntu Server 14.04 LTS image.

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:

  • Ubuntu 16.04 should have Python 3.5 already installed.
  • 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

curl http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_2_0.tar.gz > segemehl_0_2_0.tar.gz
tar xzf segemehl_0_2_0.tar.gz
cd segemehl_*/segemehl/ && make && cd ../../

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

sudo cp segemehl_0_2_0/segemehl/segemehl.x /usr/bin/segemehl.x
sudo cp segemehl_0_2_0/segemehl/lack.x /usr/bin/lack.x

... or the bin folder of your home directory:

mkdir ~/bin
cp segemehl_0_2_0/segemehl/segemehl.x ~/bin

3. Install DESeq2

Start R:

R

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

source("http://bioconductor.org/biocLite.R")
biocLite("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 pip3 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